Amphibians are rapidly declining worldwide, but recent studies have shown that their diversity may be heavily underestimated, and many new species have been recently reported from biodiversity hotspots. For successful conservation and management strategies to be implemented within such hotspots, a better understanding of the species diversity and their evolutionary relationships is required. We used three mitochondrial (16S, 12S and CO1) and two nuclear (rag1 and rhodopsin) gene fragments to investigate the genetic diversity within the endemic Indirana genus from the Western Ghats biodiversity hotspot. The species diversity within Indirana was found to be much higher than previously anticipated. Instead of the expected six species within this region, our analyses identified 11 clades with high (4.2–17.1%) sequence divergence. Each of these clades is likely to represent a distinct species. Particularly pronounced polyphyly was found within Indirana beddomii, which consisted of four highly supported monophyletic clades with high genetic divergence. Similarly, Indirana diplosticta was divided into two highly divergent monophyletic clades. We also report a new candidate species within the genus from Vellarimala in Kerala, which we believe is yet to be described. Our results suggest the existence of multiple unrecognized cryptic lineages within Indirana, all of which are likely to have more narrow distribution ranges and lower abundances than the taxonomic units into which they are currently assigned. Hence, the International Union for Conservation of Nature (IUCN) Red List statuses of Indirana frogs are likely to be in need of substantial revision, and detailed genetic studies across the Western Ghats might uncover additional new candidate species from this poorly studied endemic genus. Together with several earlier amphibian studies describing cryptic species from tropics, our results highlight the importance of proper species identification efforts before it is possible to reliably determine the IUCN conservation status of tropical amphibians described on the basis of morphological criteria.