The mountainous Western Ghats are part of a biodiversity hotspot and extend for about 1600 km, lying close and subparallel to the west coast of peninsular India. The region is a centre of diversity for amphibians, and recent preliminary work on some components of both caecilian (Gymnophiona) and frog (Anura) fauna is indicative of a high degree of local endemism. We investigated diversity in mitochondrial rRNA 12S and 16S sequences for long-tailed, unstriped Ichthyophis (Amphibia: Gymnophiona: Ichthyophiidae) that potentially represent four taxonomically confused and poorly known endemic caecilian species. Data were analysed for18 individuals from along c. 1500 km of the Western Ghats region. Genetic diversity is remarkably low, with a maximum uncorrected p-distance of 0.5%. These DNA sequences and new morphological data do not allow us to reject the null hypothesis that the sample comprises only a single, widely distributed, highly interconnected species. The phylogenetic signal among the data is extremely low. However, population genetic analyses reveal that the Palghat Gap, a c. 30 km discontinuity in the Western Ghats considered to be significant in the biogeography of other organisms occurring in this region, corresponds to a significant subdivision of long-tailed, unstriped Ichthyophis into two groups.