Though the legends related to the origin of a place cannot be deemed as its history, the story on the evolution of Mannarasala as the supreme place of worship of the serpent Gods is associated with Parasurama, the creator of Kerala.
The history of Mannarasala has been mentioned in the 'Mandara Salodayam' Sanskrit poem written by Mannarasala M.G.Narayanan Nampoodiri of the sacred family, who wrote it on the basis of reliable accounts and legends traditionally handed down and in the light of old books available with the temple. Since the poem was incomplete, the history narrated here is from the book 'The Serpent Temple Mannarasala', published by Mr.N.Jayadevan of Manasa Publications (Translated to English by the renowned scholar Dr.Ayyappa Panikker). This book is also based on the advice and instructions received from the former Great Mother, and in accordance with the other members of the family as well as the old records examined for the purpose.

Sree Parasurama decided to seek release from the sin of killing the Kshathrias. He approached the holy Rishis. They suggested that he should make a gift of a land of his own to the Brahmins. Parasurama, the son of Bhrigu, propitiated Varuna Deva (the Lord of the Seas) to get some land for himself. He threw into the sea the axe which Paramasiva had given him with his blessings. Thus he raised the land from the sea and gave it as a gift to the Brahmins according to the rules. This land came to be known as Kerala. That piece of land was not habitable because of the salinity. Not even vegetables grew there. People began to leave the place. Bharghavarama was pained at this. He undertook penance to please Lord Siva, who advised him that the objective could be realized only if the flaming poison of the serpents was spread everywhere and that the only means of doing that was the worship of Nagaraja.
Parasurama, a Yogi, firm of will and above all desire, decided that he would take no rest until he saw Kerala come up as a land of evergreen beauty full of trees and plants, prosperous in every way. He set out with his disciples in search of a deserted jungle in order to please Nagaraja who was inaccessible and beyond anybody's understanding. He found a suitable place near the seashore in the southern part of Kerala. Satisfied with having found a proper place for the realization of his cherished dream, the great Rishi constructed a Thirthasthala for the performance of penance. Bharghavarama, a partial incarnation of Lord Vishnu, had to undertake very severe penance.

Nagaraja, who was pleased, appeared before Parasurama, willing to grant him his desire. According to the poem by Mannarasala M.G.Narayanan Namboodiri, the Nagaraja made his appearance as if :
" The unspeakable splendor of millions of moons! The bright magnificence of emeralds stuck to the hoods. Golden jewels made attractive by miraculous embroidery! Lotus feet worshipped by crowds of Gods! Brilliant beauty of form, full of youthfulness!".

Parasurama prostrated at the lotus feet of Nagaraja and prayed to realize his objective. Nagaraja granted his request with great pleasure. Ferocious serpents arrived at the spot at once to spread the flaming Kalakuda poison. Because of the percolation of poison, the land of Kerala was desalinated, to become habitable with envious greenery.
Parasurama then requested the Lord to bless the land forever with his eternal presence, and that was also accepted by the kindly-disposed Nagaraja.

At a very auspicious moment Bhargavarama, the supreme devotee, installed, according to Vedic rites, Nagaraja, who is Brahma, Vishnu and Siva in one in the 'Thirthasthala' (Hall of pilgrimage) filled with Mandara trees, the place now known as Mannarasala. (The installed deity here represents Anantha (Vishnuswaroopa) and Vasuki (Siva in spirit). The installations of Sarpayakshi, Nagayakshi and Nagachamundi, the Naga deities, as well as of their associates were conducted in the proper places with the proper rituals. Parasurama performed to the accompaniment of Vedic recitation and singing of Sama, Abhishekam, Alankaram, Neivedyasamarpanam, Neeranjanam, Sarpabali and other rites pleasing to the serpents and thereby made all the serpents happy.
Parasurama brought learned people from other religions; installed Durga and other deities in different places; appointed Brahmins who were Thanthric experts for performing poojas; nominated Kshathrias, peasants and the Ashtavaidyas who were supreme among the physicians; thus he brought Kerala, filled with beautiful vegetation and to prosperity.

After giving important instructions to be followed to preserve the sanctity of the place, Parasurama left to do tapas on Mahendra Mountains.

Many generations passed by. The family fell into the grief of childlessness. Vasudeva and Sreedevi were the sad couple who had to bear that heavy load of sorrow, who resolutely worshipped Nagaraja to allay their grief.
It was about this time that unexpectedly fire broke out in the jungle around the dwelling place of Nagaraja and burnt down the jungle. The serpents were tortured by the flames, forcing them to hide in their pits with great difficulty.
Vasudeva and Sreedevi looked after the serpents, who had their hoods charred, bodies half-burnt, and fainting from time to time, falling down and crawling along. They gently fanned them with fans made of sweet-scented grass and poured ghee mixed with honey and oil on the wounds; cooled their melted bodies with sandalwood ointment; and comforted them. They put them at the foot of banyan trees. They performed purification ceremonies and consecrated the pits; and were put up in special places under the shade of deodar trees and in Chitrakudas.
The couple performed abhisheka with thirtha like Panchagavya (a holy mixture of five items from the cow's milk, curd, butter, urine and dung); observed elaborate poojas according to rules with areca nut flower bunches, fragrant flowers and water, incense etc., Nivedyam with melted butter (ghee), milk, payasam with molasses, rice powder, turmeric powder, coconut juice, Kadali fruit, cow's milk, all mixed together in the proper form as Nurum Palum, equivalent to the elixir of life. They offered serpent deities with great devotion, appam, aval (beaten rice or rice wafers), tender coconut etc. They chanted vedic mantras, performed circumambulation and performed all kinds of poojas to restore those crowds of serpents to full health.

The omnipresent and omnipotent Nagaraja was greatly pleased with their continuous penance and the love shown to his associates; Nagaraja made himself visible to the couple and blessed them that he would incarnate on the earth as their beloved son. He said " I shall assume the form of a serpent and stay here (in Mannarasala) permanently, as long as the sun and the moon are there, showering prosperity on your family and granting protection to all the devotees who come here …".
Thus Mandarasala, the place filled with Mandara trees, the holy spot where the serpents got shelter, where the earth was fully cooled, became Mandarasala.
The boon came true. The Brahmin lady became pregnant and gave birth to five-hooded serpent-child as well as a human child. The two brothers grew up together. Initiation ceremonies and Vedic education were carried out at the proper time in the traditional style. Nagaraja instructed the younger brother to enter into matrimony for the perpetual reservation of the holy family and he obeyed it. When the five-hooded Nagaraja realized that the objectives of his incarnation were realized, he informed the Holy Mother that henceforth he would live at this Illam by entering into Samadhi to bless the devotees. Then he suggested certain inviolable rituals and rules for offering worship and then went into the immaculate cellar and vanished.
(It is believed that even today that five-hooded Nagaraja stays in the cellar doing Tapas for the abound prosperity of his dependents. The members of the household always refer to him with great respect and devotion as "Muthassan' and "Appoppan" (Grand father). The jungle close by is the exclusive preserve for his unobstructed peregrinations (Appoppan Kavu - Grandfathers' Grove).