Thirunelli temple is located at an altitude of about 900m in north Wayanad in a valley. It is situated around 32 km away from Manathavady. The exact history of the temple is not known. However Thirunelli was once an important town and pilgrim centre that was surrounded on four sides by mountains. There is proof that Thirunelli at the time of Chera king Bhaskara Ravi Varma I (962-1019 CE) was an important town and pilgrim center in south India.

The name Thirunelli derives from the nelli, which means Indian gooseberry. The Matsya Purana, Skanda Purana, Narasimha Purana, Padma Purana, and many other Puranas and Hindu texts mentions this temple as being built by Lord Brahma, located in the picturesque Sahya valley and it is referred to as Sahyamalaka Kshetra. It is believed that the famous incarnation of Lord Vishnu Parasurama visited Thirunelli and performed last rites at the death of his father sage Jamadagni.

Kottiyoor Temple and Trisillery temple have been linked with legends of Thirunelli temple. Papanasini is a holy mountain stream that is around 1 km North West of the temple premises. It is believed that one dip in the cold Papanasini waters in reputed to wash away all sins. It is also believed that Papanasini is the confluence of river Ganga and Saraswathy. Panchatheertham is the holy temple pond. The temple has no well in its premises. Therefore water is transported from a perennial mountain stream deep in the valley through impressive stone aqueducts into the priest`s room. This place is a well known destination to perform last rites of the deceased at the rock close to Papanasini stream.

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