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Background  Phylogeography and historical demography of the cyprinid fish  Diptychus maculatus  (subfamily Schizothoracinae) are evaluated across three river systems in the Northern Qinghai-Tibetan Plateau (QTP) and Tien Shan range: the Indus River, Tarim River and Ili River.    Results  Results from both mtDNA (16S rRNA, Cyt  b  and D-loop) and nucDNA (RAG-2) resolved four reciprocally monophyletic clades, representing populations from Indus River, South Tarim River, North Tarim River and Ili River, respectively. The divergence times was estimated to be 1.5–2.5 Mya. It is consistent with the hypothesis that the split of four clades is the consequence of vicariance resulting from both the intensive uplift of QTP and Tien Shan as well as the resultant expansion of the Taklimakan Desert. Several lines of evidences indicate dynamic demographic histories for the populations, with late Pleistocene and Holocene population bottlenecks and expansions except the Indus River.    Conclusions  Our results clearly depicted the phylogenetic relationship of  D. maculatus  from Indus River, Tarim River and Ili River. The analyses implicated the relationship among the distribution of  D. maculatus , paleo-drainages and geographic events, and implied the existence of the South Tarim River in history.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-016-0756-3) contains supplementary material, which is available to authorized users.

Phylogeography of Diptychus maculatus (Cyprinidae) endemic to the northern margin of the QTP and Tien Shan region