With the recent classification of red panda into two phylogenetic species, we propose ‘Siang river’ as a potential boundary for species divergence between the Himalayan red panda (Ailurus fulgens) and the Chinese red panda (Ailurus styani). Bayesian-based phylogeny and MJ network splited all the sequences of red pandas into two distinct clusters in accordance with the origin of the samples collected from the east and west side of the Siang river. The clade 1 that represented Himalayan red panda was formed by the inclusion of samples originated from the north West Bengal, Sikkim, and central and Western Arunachal Pradesh and South Tibet, located in the west of Siang river. While, clade 2 stood to Chinese red panda, and represented samples originated from Dibang valley of eastern Arunachal Pradesh, India and Southwest China, in the east of Siang river. This study provides pragmatic genetic evidence and demonstrates Siang river as a potential boundary of species divergence in red panda by contributing samples from Indian Himalayan Region. We suggest being associated with diverse habitats, threats and transboundary distribution, both species of red panda require regional as well as transboundary level conservation initiatives and multilateral cooperation for a species survival plan.