We describe a new species of Agasthyagama from Idukki district, Kerala, India. The new species is distinguished from its sister species Agasthyagama beddomii by a combination of scale characters and are also genetically different from each other with 11% uncorrected pairwise difference in ND2 gene and 3% in 16S gene. The two species are also geographically separated, the closest distributional records are approximately 80 km apart.