The temple is one of the 12 Jyotirlinga shrines and the current structure is built in the 12th century by the Pandya dynasty. There are 64 Theerthams (holy water bodies) in and around Rameswaram. Bathing in these tanks is a major aspect of the pilgrimage to Rameswaram and is considered equivalent to penance. 22 of the tanks are within the Ramanathaswamy Temple. The foremost one is called Agni Theertham, the Bay of Bengal. Villoondi Theertham literally translates to 'buried bow', is believed to be the place where Rama quenched the thirst of Sita by dipping the bow into the sea water. Other major holy bodies are Jatayu Theertham, Hanuman Theertham, Sugreeva Theertham and Lakshmana Theertham.
Gandhamathan Parvatham, a hillock situated 3 km from the temple has Lord Rama's feet as an imprint on a chakra (wheel).