The Southern birdwing butterfly, Troides minos Cramer, 1779 is endemic to Western Ghats. This has many synapomorphic features with other members of Troides butterflies in Southern Asia. Here we report the partial sequence of mitochondrial cytochrome oxidase subunit I (COI) gene of T. minos, isolated from Northern Kerala (GenBank Accession Number: HQ424201.1). The sequence analysis of the COI DNA revealed that Troides minos, is closely related to Troides aeacus and Troides helena isolated from Indian subcontinent and they were evolved from the similar ancestors. The divergence of Troides butterflies of Asia began before the joining of Indian Plate with Eurasia and the rise of Himalayas. Molecular data the supports the existing view of origin and distribution of their ancestors from Northern hemisphere to the Indian subcontinent and Indonesia. The COI sequences of T. minos also demonstrate that their species diversification took place after the rise of Himalayas. The results of the present study also indicate the divergence of Troides butterflies of Indian subcontinent and endemism of T. minos in Western Ghats are associated with the loss of continuity in distribution of their ancestors as they become extinct in Deccan Plateau. The extinction of Troides population in Deccan Plateau was associated with the climatic changes resulted from the vicariance events like rise of Himalayas and disappearance of Tethys Sea.