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Originally this was a Raja Gopalan temple. Gopalan is seen facing South with Rukmini, Satyamabha and Shengamala Thaayar.

During the rule of Sarobhoji Raja of Thanjavur, it is believed that the idols of Rama and Sita were found under a Fig Tree in Thiruthuraipoondi Taluk.

 Sarabhoji Raja, whose plan was to take it to Thanjavur, is said to have installed the deities in Vaduvur and built the Kothandaramar temple, on the request of the people of Vaduvur.

Kothandaramar, at Vaduvur, is seen as a handsome Lord (like the Raja Gopalan of Mannargudi) with a bow and arrow. 

There is also a separate Sannidhi for Hayagriva facing North. 

After completing the forest life of 14 years, Lord Rama prepared Himself for the journey to Ayodhya.  

The sages of the forest requested the Lord to stay with them for ever.  He promised them to fulfill their request the next day.  Lord made an idol of Himself.

The sages, who came to see Lord Rama next morning lost themselves at the beauty of the idol and desired to have it for themselves. 

 Lord Rama, as if He knew nothing about the idol, asked the sages that they liked the idol more than they liked Him. 

Allured by the beauty of the idol, the sages said Yes.  Lord Rama gladly gave them their wish and returned to Ayodhya.

The idol, after thousand of years reached the hands of the devotees in Tirukannapuram.  

They also made other idols – Mother Sita, Sri Lakshmana and Sri Anjaneya.  During foreign invasion, they hid the idols in a place called Thalai Gnayiru.  

 Lord Sri Rama appeared in the dream of King Sarfoji, ruling then the Thanjavur region and directed him to build the temple for Him, indicating also the place.  

The king went to Thalai Gnayiru, took the idols and on return stayed at Vaduvur for a while. 

Many devotees met the king and requested him to install the idols in Vaduvur.  

Responding to the wishes of devotees, the king left the idol with them.