A good percentage of mainstream Hindu deities as such are worshipped in Kerala. There are indeed conceptual differences in style of worship as well as its associated myths.
Kerala was originally part of the erstwhile Dravidian culture that was common around South. So many Dravidian concepts were strictly followed and worshiped as such. It must be noted, Vedic Hinduism or Brahminical version of Hinduism came much later. It was mostly after the 5th-8th century AD period, Brahminical Hinduism became mainstream. And one way it became popular, through acceptance and absorption of existing culture and faith into its Vedic traditions. So many deities and gods which were originally worshipped outside the Vedic Hinduism became part of it to such a degree, that its inseparable from Hinduism in Kerala. This includes even Buddhism and Jainism which was popular untill the rise of Brahminical faith
And due to it, such deities are seen only in Kerala or its nearby places, not much outside.
The key deities that are worshipped are;
Krishna/Vishnu
The pictorial concept of Thiruvambady Krishna in Thrissur. Its one of the few temples that have Krishna idol as such as its deity and worshipped mostly as Baby Krishna
Krishna is indeed the most popular deity worshipped across Kerala. Its a god, which majority of Hindus in Kerala identify as close to heart. Krishan is mostly worshiped as either Baby Krishna (Unni Kannan) or as a kid or in teens. There are very few temples where Krishna is worshiped as an adult or as Dwarakadesh (Lord of Dwarka) or in his warrior form or as charioteer form. There are only two or three temples in Kerala, where Krishna is worshipped as Parathasarthy (charioteer of Arjuna). Generally Krishna is worshipped as alone. There is no concept of worship of Radhakrishna or Krishna-Rukmini/Satyabhama etc in Kerala.
One interesting part is that majority of Krishna temples actually have an idol of Lord Vishnu as such. There are only very few temples which have idol designed in form of Krishna.
This is primarily because in Kerala’s sole worship form- Tantra; there is no specific way to invoke Krishna as such. Tantra as such deals with the release of divine energies and control of it. Krishna as such is a sub-identity of Lord Vishnu as Krishna alone has no identity outside that of Vishnu. So every rites and mantras are related to Mahavishnu and hence most of the idols are that of Vishnu (in form of Chaturbahu Vishnu- The four-armed Vishnu).
The much popular Guruvayurappan- the Lord of Guruvayur temple
However there is a concept of assumption, ie devotees are free to assume the deity as to the form they like and over a period of time, many assumptions have become strong enough to give an identity as such. For example, the famous temple of Guruvayur is internationally renowned as Krishna temple, but the deity in the temple isn’t Krishna, rather Mahavishnu and every rite is done in name of Lord Vishnu. But devotees for a period of time assumed and widely believe its Lord Krishna there and worship the deity praying as Krishna despite seeing the deity in Lord Vishnu’s form. Its a classic case of assumed identity.
There is a reason for this historically. Since 8th century, Brahminical Hinduism was growing rapidly and it pushed for the rise of Brahminical powers that started gaining its foothold over the rapidly declining Chera Empire. A good percentage of Brahmins and their supporters (the Nair Lords) were into Vishnu worship (Vaishnavas). The Nampoothiris were hardcore Vedic Brahmins and Vishnu is essentially linked to the identity of Savitr, a key Vedic deity that accepts the Ahavisu (Vedic offerings) offered to the Gods in the sacrificial fire. In addition, Cheras as such was widely Shaivates, hence the rising Nampoothiri cult focused on building more on Vaishnava temples as a venue for their cultural rites.
Post end of Chera Empire in 12th century and the rise of Brahminical Kingdoms/feudalistic orders, Vaishnava culture got an official status and thus there was a heavy patronage in building and worshiping Lord Vishnu extensively. Most of the royal families in Kerala started identifying Vishnu as their protector deity and hence royal temples started coming up with Vishnu as the main deity.
By 15th century, Bhakti movement has started and the movement aggressively focused on the worship of Krishna cult. One reason with Krishna was primarily because the lord is easily identifiable to a much larger society. He can be one’s own baby whom we can cuddle or a kid in our house with whom we can play or a teenager with whom we can fall in love or as a great King whom we can seek protection as well as a great philosopher whose philosophies (Gita) can guide us. In short, Krishna is a better divine identity which all segments of society can easily identify much more than Vishnu which is more related to Vedic concepts. The popularity of numerous Bhakti literature, starting from Ramayanam to Krishnagatha or Narayeenam to Kuchelavritham, had made a huge impact over devotees that led to the growth of Krishna worship cult. Infact even today, almost every commoner irrespective of their religion or caste knows some part of much renowned Njanappana which we call as Malayalee’s Bhagavat Gita. These works helped to reinforce a strong Krishna worship cult among devotees that made many Vishnu temples to be assumed as Krishna temples, which still continues.
The national deities of two kingdoms of Kerala, Sree Poornathrayeesa of Cochin and Sree Padmanabha of Travancore, both being forms of Lord Vishnu.
Saying so, Vishnu identity as such is also worshiped in many places. Infact we have a case where Lord Vishnu was identified as Emperor of Travancore and the kingdom ruled in his behalf. The National deities of Travancore and Cochin Kingdom were Lord Padmanabha and Lord Poornathrayeesa, respectively both being in the identity of Lord Vishnu as such. The much well-known temple of Navamukunadan on banks of River Nila which represents the venue of the coronation of Kerala Rakshapurushan (Protector of Kerala) in medieval times for which endless wars and feuds were fought, is also Lord Vishnu in his original form. So essentially Vishnu/Krishna worship is so strong in Kerala. Even today, the official emblem of Kerala State is the Counch (Shanku), that represents Lord Vishnu.
Apart from these identities, there are very limited temples meant for other forms of Vishnu like Rama, Parasurama, Vamana, Narasimham etc which aren’t much popular as such.
Shiva
Ernakulathappan, Lord Shiva as protector of Ernakulam (Kochi city)
Shiva is the second most popular deity in Kerala after Vishnu/Krishna. There are numerous Shiva temples in Kerala. Shiva as such was seen as the imperial god during times of Chera empire. Chera Emperors were adherent worshippers of Shiva and the official religious identity in times of Chera was that of Saivaite. Due to this, several grand Shiva temples were commissioned during the reign of Chera empire. This explains why much of Shiva temples in Kerala are so ancient.
Thiruvanchikulam, the most ancient Shiva temple in Kerala, regarded as the Imperial temple of Cheras
The imperial temple of Chera Empire was at Thiruvanchikulam near Kodungallor (near to Kochi) which was referred to as Vanchi, the older name of Chera Empire. Due to this factor, even after the disintegration of Chera Empires, the identity of much smaller the Travancore Kingdom was that of Vanchi and their official National anthem was Vancheesamangalam (Salutations to Lord Vanchinathan- Shiva) which was bit ironical as their national deity was Lord Vishnu in form of Padmanabha.
Zamorins of Kozhikode have consecrated Lord Shiva (Trivikrameswaran) as their royal deity for their capital city of Kozhikode which is now the famous Tali Mahadeva temple in the city center, though Zamorins were Vaishnavites and identify Guruvayurappan as their national deity.
Mostly we have temples only in identity as Lord Shiva itself. We rarely worship any other form of Shiva like Bhairava or Rudra or Daksinamurthy etc. Kerala has its own tradition of 108 Mahasivakshetrams or Great Shiva temples.
The extremely popular 4 ancient Shiva temples in clockwise direction- Peruvanam in Thrissur, Ettumanoor and Vaikom in Kottayam, Tali in Kozhikode
Shiva temples in Kerala are divided between Tali and Normal temples. Tali is a term given by Brahmins to those Shiva temples which they built or taken over from Cheras identity (read as Dravidian identity). As much of Shiva temples were originally built in Chera period, at the same time, Nampoothiris also built Shiva temples in Vedic style which they called as Tali. However such distinction is vague today as all Shiva temples were absorbed into the Tantric cult and there are only a handful of Shiva temples that follows outside the standard traditions.
Ezhava Shiva, as installed by Sree Naryana Guru that highlights the value of universal brotherhood sans caste or creed or religion.
Lord Shiva also played a key role during Kerala renaissance period when the famous reformer Sree Naryana Guru installed the first Non-Brahmin temple in the modern period. He consecrated an idol near the river banks at Aruvikkara in 1888 and when Brahmins questioned the legitimacy of a low caste consecrating a temple, he replied that he has installed an Ezhava Siva . The concept of Ezhava Shiva or Low caste Shiva played a key role in Kerala renaissance as it pushed the concept that God is much above casteism. The 4 lines which Guru wrote below the Shivalinga has captured the attention of entire Malayalees and gave a push for progressive ideals of Renaissance
JAATHIBHEDAM MATHADWESHAM EATHUMILLATHEY SARVARUM SODARATHWENA VAAZHUNNA MATHRUKASTHANAMANITHU
meaning- This model place is an ideal dwelling of all those who have no religion or caste, rather with a universal brotherhood.
Bhagavati
Bhagavati/Devi as in Kumaranellore in Kottayam
The third most popular deity across Kerala is Bhagavathy which merely means Goddess. A very unique factor associated with Devi worship is that we have very less number of specific devi cult. Say there are very fewer temples dedicated to the specific goddess like Lakshmi, Saraswati, Durga etc, rather its almost all dedicated to Mother Goddess- Bhagavathy. According to each occasion or festivities, the Bhagavati is assumed to take various forms, like that of Lakshmi-Saraswati etc. However, the worship as such is in common form.
However, there are several Parvathy Shrines as such. This is because, in Shiva temples, Parvathy as such is worshipped separately, mostly in a separate sub-shrine located right behind Shivalinga. In such cases, the identity- Parvathy as such is highlighted.
The concept of Balabhadra or Mahabhadra, a form of pacified Kali which is widely worshipped across Kerala as Bhagavati
Traditionally Kerala had a strong Bhadrakali worship cult. Much of the many popular Devi temples had a history of worshiping Kali as such in the ancient period. However, in tantric order, worship of Kali in her fierce form wasn’t recommended. It needed highly dedicated Nampoothiri priests who must be proficient enough to invoke Kali’s energies and control it as the belief is that any mistake in the rites can result in backfiring to the invoker. Due to this reason, the majority of Nampoothiris weren’t comfortable to worship Kali, hence the deity got pacified, reducing either to just Bhagavathy or as Balabhadra (a pacified form of Bhadrakali, pronounced as Belabhadra). Most of Bhagavathies are regarded as some form of Bhadra as such, but not Kali.
Choothankikkara Devi, one of the famous temple where the devi is considered to be in Trinity form, ie Saraswati in late night and early morning, Lakshmi in morning hours and Bhadra in evening.
Majority of Devi temples are considered to be trinity form of Devi. There is no concept of independent Lakshmi worship as one finds in North India as Lakshmi is combined with Vishnu worship or with Bhadra in Devi worship (hence the popular Devi chanting- Amme Naryana, Devi Naryana, Lakshmi Naryana, Bhadre Naryana).
Durga form of worship is also limited, but many royal families and warrior families do have family temples were Devi is worshiped in Warrior form. Infact due to vagueness in the definition of Bhagavathy, in many places, the goddess was assumed as the form of Durga, especially Balebhadra/Mahabhadra temples.
Sapthamathakal or Seven Mothers as worshipped in many temples.
Many temples in Kerala worships Sapthamathakal (the seven mothers) as sub-deities.
Kodungalloor devi, the fierce form of Kannagi similar to Bhadrakali as worshipped in Kerala
And in Kerala, Kannagi worship is very common. We believe, the heroine of Silaprathikkaram- Kannagi as a form of Bhadrakali and widely worshipped in Kerala. Infact many Bhadra temples have local myths linking to the story of Kannagi as such. The famous Attukkal temple in Trivandrum and Kodungallor temple are some of the extremely popular Kannagi shrines worshipped in the fierce form of Bhadra.
Komarams or Oracles are seen in many temples as part of old Dravidian traditions where they get into a trance-like state when they become Devis.
Due to this reason, the Chilambu (Anklets) and Pallival (The curved Sword) are regarded as the symbol of Devi and widely worshipped as such. The ancient Dravidian tradition of Oracles (Vellichapadu) where humans get into trance-like state due to being blessed by Goddess and their divine prophecies is also a widely respected tradition, especially in Malabar side.
Pallival and Chilambu, regarded as the symbol of Devi in Kerala, is widely worshipped as such.
Sasthavu
Sastha or Dharmasastha is a very popular deity in Kerala. Infact it's very specific to South Indian traditions, especially Kerala-TN-Karnataka-AP regions.
The 8 forms of Dharmashatha as popularly worshipped in Kerala-TN
This tradition, however, is not part of Vedic Hinduism, rather part of Buddhist traditions of the past. Historically since the 3rd BC era, Buddhism and Jainism have gained a stronghold in South India, especially among upper strata of society. Buddhism had more popularity due to its liberal traditions when compared to comparatively harder Jainism. Sastha as such means Teacher as in Pali language which later adopted into Sanskrit and Old Tamil. So essentially Dharma-Sastha as such was a reference to Buddha- the eternal teacher of Dharma. However, over time, it got a concept of God (contrary to Vedic concept of Yama- the God of Dharma).
Hindu concept of Ayyappa/Sastha as Hariharasudhan or Son of Shiva and Vishnu in Mohini form.
There were intense worship traditions for Sastha in various forms across the South as Ayynar, Ayyappa, Cattan etc. However across South, with the rise of Brahminism, particularly in the 5th century, there was a degree of shared philosophies and the concept as such was slowly adopted into the Vedic concept which is reflected in the 7th-century work- Brahmanda Purna where Ayyappa slowly got a Vedic identity as Hariharasuthan (son of Shiva-Vishnu).
The most popular Sastha temple is that of Sabarimala Ayyappa, which has become the venue of world’s largest annual pilgrimage with nearly 40 Million pilgrims praying to the lord.
The rise of Cholas in South has also pushed for the growth of Ayyappa/Sastha as a Hindu deity, thus losing the last bit of its erstwhile Buddhist identity. Taking the cue from Chola tradition, Pandyas strongly worshipped the deity which sooner got transmitted into Chera Empire. Pandya princes (who later formed Pandalam-Poojnar dynasties in Central Travancore) who migrated into Kerala over a period of time essentially became flagbearer of this legend in its Hindu identity. In this period of the 9th-10th century, there was a rapid growth of Brahminical culture in Kerala and one approach of strengthening Brahminical supremacy was to absorb existing traditions into Brahminical Hinduism. Many Buddhist and Jain Temples soon became Hindu temples and the deities also absorbed within Vedic Hindu realms. Sastha effectively became part of this absorption process.
Vettakkuorumakan, a different form of Ayyappa as worshipped in Malabar and North Eastern parts of Tamil Nadu.
Multiple versions or concepts of Sastha became popular and some of them like Vettakkuorumakan (Divine Hunter) even became the family god of Chirakkal Kolathiris of North Kerala. So as Dharmasastha as such became a very popular god as equal to as Ganapati, by having a sub-shrine in almost all major temples across Kerala.
As Nampoothiris find hard to explain the difference between Vedic god- Yama (Hindu God of Dharma) and Dharmasastha (Adopted as God of Dharma in South), essentially the concept of Yama was slowly diminished in Kerala as mere God of Death and to some extent also got Tamasic shades (Negative shades). Many elements of Yama worship as done in Vedic period, got associated with Ayyappa/Dharmasastha like burning Niranjam (Coconut lamps) or wearing the black dress (which effectively became the spiritual holy color) or Dharmasastha’s relationship with Saturn (Shani) etc. So effectively Yama worship almost got eliminated in Kerala and effectively replaced by Dharmasastha.
Nagas
Naga worship as in Kerala
Kerala has an extraordinary concept of worship of Snakes. Nagas/Sarpas hold a key position in Kerala’s worship culture. Almost 99% of Kerala’s temple have a sub-shrine to worship Nagas and in past it was very much worshipped in homes of the majority of upper caste families by having a snake grove (Sarpakkavu)
Naga worship is often associated with Keralopathi (formation of Kerala) as Parasuram sought the help of Snake King Vasuki to clear the salt mountains of Kerala which rose from the seas. In return, Vasuki and his Naga race got permanent right to reside across the new land as their own, so as with responsibility to protect the land. Due to this concept, Snakes are extremely revered in Kerala as they are believed to part of the family. As per belief, each family has their own protecting Snake family and their divine presence is essential for that family’s prosperity and fertility.
Snake King and Queen with the entire army of Snakes as worshipped in some temples
Typical Snakegrove (Sarpakavu) as worshipped in homes etc. Snakes are traditionally worshipped in a forest like ambiance. And as they belong to the family, houses are also constructed (called as Chitrakoodam) which denotes for a dwelling space for Snake Family.
As a concept, we don’t worship just Snake God- Vasuki alone. Rather we worship entire Snake race (Sarpakula) as such. This means every family or temple has their own Snake family that is typical like one’s own human maternal family- Brother, Sister, sister’s children etc. Snake lineage is considered as Matrilineal, hence it worked much like how upper castes lineage moved. So in each family, they worship their snake family’s elder brother and sister. Some even have local names much like humans.
The pictorial concept of Nagaraja (Vasuki) as on left and Nagayakshi on right
In divine concept, we worship Nagaraja (Vasuki) and his sister Nagayakshi (Manasa). Nagaraja and Nagayakshi always be worshipped with their Generals (assistants) of Snake army represented as ordinary snake idols as well as with Chitrakoodam (snake house). In some places, Nagayakshi is believed to be the wife of Nagaraja with Nagachamudi as the sister.
Naga worship as in Manarashala temple with Nagaraja in the center and Nagayakshi and Sarpayakshi on side accompanied by Takshaka (General of Snake Army) behind to Yakshi.

Manarashala temple is the only temple to have a Priestess to do the pooja as Nagaraja was born here and he was extremely attached to his mother. Hence the senior lady of the house is considered as the mother of snakes (Nagamatha or Amma as popularly known) and she has the only right to feed the snake family.
Nagamatha or Amma holding the baby Nagaraja during the Ayilam festival in Mannarashala temple.
There are few dedicated Snake temples. The most famous being Mannarashala temple which is believed to be a place where Nagaraja was born as a baby boy to a Nampoothiri family. Due to this tradition, Manarashala is often regarded as the most celebrated Snake temple in Kerala. Apart from this, Pambummekkattu temple near Thrissur is regarded as one of the oldest temples, believed to be first places where Nagaraja has manifested his divine form. There is also a dedicated temple to Nagayakshi in Vettikkottu near Kollam. The famous Nagercoil temple in Kanyakumari was also a celebrated temple dedicated to Snake king, which has gone to TN after Kanyakumari was transferred.
As a concept, Nagas are believed to be protectors of fertility, hence heavily worshiped by childless couples for restoring their fertility. The curse of Nagas/Sarpas is regarded as the most dreaded, that can affect around 7 generations of a family and destroy the fertility and eyesight. Due to these factors, Naga temples are regarded as a sort of place for the redemption of their sins that may be classified as Nagadosa. Turmeric, milk are the main offerings to Nagas.
These are the key deities worshipped in Kerala.
Then every temple has a sub-shrine for Ganapati as such. Individual Ganapati worship is too low, though every pooja or homa starts with invoking Ganapati thro’ Ganapathi Homam.
Ganapathi is more worshipped in form of worshipping elephant as such. Festivites like Annayottu or Mass feeding of Elephants are very typical to Kerala as to celebrate the happiness of Ganapati thro’ elephant worship
Kerala has a Muruga worship as such, though it's not extensive as like in neighboring Tamil Nadu. There are few famous Subramanian temples (Muruga as such is called Subramanian in Kerala), but the cult is not extensive. This is primarily because Malayalees believe that Murugan lives in nearby Palani hills and hence don’t find enough myths to connect to local places. Due to this reason, we visit Palani commonly rather having many shrines in Kerala.
The famous Haripadu Subramaniyan temple. Picture was taken during the festival period when State Police makes their guard of honor to the deity.
There are certain deities that are specially worshiped like Dhanwanthari (God of Ayurveda), Sudarshana Murthy (Sudarshana Chakra of Lord Vishnu), Vishnu Maya (an occult god) etc.
Dhwanthari Moorthy- God of Ayurveda
Sudarshana Moorthy- The discus in hand of Vishnu
Vishnumaya, popularly known as Kuttitachathan is a popular god of the occult.
Another unique worship culture is that of Yakshis, Gandharvas, and demi-gods like that. The concept of Yakshi worship is very strong in Kerala and many temples have Yakshi shrines as guarding goddess. Gandharva worship was once extensive, but now got limited due to negative connotation existing around Gandharvas.
Yakshi Worship in Kerala, much similar to Naga worship as Yakshis are worship in Kavu or Groves.
Gandharava worship as seen in few places in Kerala.
One important deity which is very popular across India, but rarely worshipped in Kerala is Hanuman. Kerala doesn't have a native Hanuman worship culture. Hardly 4 or 5 temples exist in entire Kerala where Hanuman is worshipped with Malayalee rites. There are a couple of Hanuman temples in Kerala which are actually not Malayalee temples, but belonging to Tulu Brahmins, GSB Konkanis, and Tamil communities. This is primarily of the traditional aversion of Nampoothiri community to invoke Hanuman’s energy using tantric means. As the belief of fierce energy is associated with Hanuman, most of Nampoothiris don’t dare to perform any regular rites or poojas associated with Hanuman other than few who are expert in it. Even some temples that have a sub-shrine meant for Hanuman, normally priests from Embranthiri community (old Tulu Brahmins) do the rituals as they don’t have such a concept. The interesting example is in Suchindram temple located in Kanyakumari district. As the temple was part of Travancore earlier, all its deities' poojas are done in Malayalee tantric style, except for its famous Hanuman shrine. Suchindram’s Hanuman is reputed across the country for being one of the tallest traditional idol. However historically Nampoothiris don’t worship this idol due to which its Tamil Archaraks do the poojas for this idol in Tamil style.
Alathiyoor Hanuman temple, one of the very few/rare Malayalee temple for Hanuman.
Some other deities as such worshiped are Chamudi, Yogaeswaran (a form believed to be Shiva), Gullikan (another form of Shiva which is done thro’ ritualistic dance), Saraswati (there are 4 temples dedicated to Saraswati as such).
Dakshina Mookambika temple near Kochi, one of the few Saraswati temples in Kerala
Gulikan Thira, a ritualistic artform where the dancer is believed to be Gulikan, a form of Shiva
There are certain non-Brahminical concepts like Muthappan (a form of Shiva worshipped in Dravidian style). So as in Malabar, there are a lot of temples that go outside the Brahminical concept of temples, by being Kavus (Groves). In such temples, its mostly ritualistic dance performances like Theyyam etc defines the concept of deity.
The concept of Muthappan is one of the key Non-Brahminical form of worship as seen in Malabar. The tradition is famous in Parassinikadavu Muthappan temple in Kannur, which is believed to be a form of tribal Shiva, which is manifested in form of ritualistic dance. Its a concept where devotees pray to the dancer in Muthappan costume, believed to be tranced as God who hears their problems and suggests ways to resolve.
Theyyams are much similar to the concept of Muthappan. But they represent various forms of Devis who performs in front of the Kavus/Groves by becoming tranced as Goddess and helps people to resolve their problem thro’ divine prophecies.
Thirayattam is similar to Theyyam, where the dancers become gods and worshipped as deities as such
Padayani is the traditional Dravidian concept of Lord Shiva and his Bhootas dancing in front of their devotees. Its currently popular ritualistic traditions of South Kerala
However unlike TN or Karnataka, one rarely finds a huge diverse temple deity culture in Kerala, as Nampoothiris effectively streamlined and brought entire temple culture to its concept of the temple since 10th century. Due to which, the concept of roadside worship culture or makeshift temples or temples meant for certain castes etc isn’t seen as such in Kerala. Ezhava community has tried building temples outside the traditional fold under its community organization- SNDP. The original idea was to put forward a non-brahminical form of worship. However as Malayalees heavily adhere to the Tantric form of worship, soon SNDP temples got into Nampoothiri styled tantric form of worship and ended up creating its own priestly community much on likes of Brahmins with the same form of worship techniques.