The genus Nyctibatrachus is endemic to the Western Ghats, India, and includes a number of species that are highly restricted in their distribution. Nyctibatrachus kempholeyensis is an endemic species distributed in the Central Western Ghats. In this paper we describe the development of eight polymorphic microsatellite markers for N. kempholeyensis. These markers were tested for cross-amplification in other Nyctibatrachus species. In addition, we confirmed the cross-amplification of three microsatellite markers from another species, N. major. The 11 microsatellites were screened with 76 individuals of N. kempholeyensis and were found to have 3–8 alleles per locus, with observed heterozygosity ranging from 0.15 to 0.95. These microsatellite markers could be used to study population diversity across fragmented habitats, to quantify genetic structure, and to assess gene flow across the populations in this endemic genus.