Abstract: The unique geomorphology of rivers in the eastern Himalaya has long intrigued geologists, yet their drainage history remains debated. Drainage reorganization can have a significant impact on genetic differentiation in freshwater taxa. This study employs the cold-adapted fish genus Schizothorax as a biogeographic proxy to reconstruct the evolutionary history of the Yarlung Tsangpo–Brahmaputra River (YTB), with a focus on a prominent hanging valley tributary-trunk stream system. Phylogeographic analyses of mitochondrial cyt b gene sequences identified a monophyletic QTP–YGP clade comprising species from the Qinghai–Tibet Plateau (QTP) and the Yunnan–Guizhou Plateau (YGP). Within the QTP–YGP lineage, YTB species represent the earliest diverging clade. In contrast, species from the Indus and Ganges basins are more closely related to congeners from the southeastern QTP and YGP. The YTB assemblage is further subdivided into two distinct clades. Molecular dating suggests that the YTB lineage diverged from the broader QTP–YGP group during the early Late Miocene, with the two YTB clades separating in the Late Miocene. We propose that a paleo-Yarlung Tsangpo–Dingba (Dibang)–Brahmaputra river and a Yigong–Parlung–Zayul (Lohit) river were established prior to the Late Miocene and were subsequently captured by the lower Yarlung Tsangpo River—via the Siang and Zhaqu, respectively—during the late Miocene and Quaternary. The modern YTB drainage configuration was established by the late Early Pleistocene. This study underscores the importance of integrating genetic, fauna and geomorphological data to understand the complex evolution of drainages in the eastern Himalayas.

Key words: cladogenetic event, paleo‐drainage evolution, river capture, the eastern Himalayan syntaxis, Yarlung Tsangpo