The diversity of frogs and toads (Anurans) in tropical evergreen forests has recently gained importance with reports of several new species1. We describe here a fossorial frog taxon related to the African Heleophrynidae and Seychellian Sooglossidae from the Western Ghats of India. This frog possesses a suite of unique ancient characters indicating that it is a transitional form between Archaeobatrachians and Neobatrachians. Molecular clock analysis based on the nucleotide diversity in mitochondrial 12S and 16S genes dates this frog as a Gondwana relic, which evolved 150–195 Mya during the mid-Jurassic period. With this taxon, the evolution of endemism in the Western Ghats and other Gondwana break up landmasses is now dated much before the Cretaceous–Tertiary boundary. We propose that sea level surges in the late Jurassic2 isolated tablelands creating insular amphibian fauna. Reduction in area may have promoted stochastic extinctions and resulted in amphibian endemism. Our study reinforces the conservation significance of the Western Ghats as major global hotspot of biodiversity. The habitat of this endemic amphibian lineage is currently endangered due to various upcoming dam projects, which is a cause of serious conservation concern.