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Phylogeographical inferences based on multiple molecular markers from different modes of inheritance (i.e. mt DNA and nuc DNA) can help to explore drivers of current species divergence over different timescales and allow a deeper understanding of evolutionary processes. River systems and mountains, owing to their drainage networks and complex topography, are often a high priority when inferring external causes of phylogeographical patterns. Here, we selected the Chinese endemic freshwater crab Sinopotamon acutum inhabiting drainage networks across the Qinling-Daba Mountains, a watershed that divides northern from southern fauna in China, as a model species (1) to investigate whether river networks and mountain systems act as barriers in shaping the phylogeography of freshwater crabs and (2) to test the impact of historic environments and ecological habitats on crab distribution. Phylogenetic tree and network analyses based on mt DNA revealed divergence between eastern and western populations, but microsatellite DNA did not recover this. Frequent and male-biased gene flow is evident. The adjacent tributaries, such as Weihe River 1 and Hanjiang River 1, although isolated by Qinling Mts, have low genetic variation in mt DNA. In addition, microsatellite DNA showed low variation between all rivers. Frequent gene flow, genetic variation and mitochondrial genetic structure in S. acutum indicated that the Qinling-Daba Mountains have had no effect on divergence in this species; instead, hydrological networks across these mountains serve as a continuous migration corridor for these crabs. Glacial refugia are probably responsible for the initial isolation of the eastern and western clades, and local adaptations after dispersal have further driven divergence. Cytonuclear discordance in phylogeographical patterns may be attributable to ongoing male-biased gene flow. [ABSTRACT FROM AUTHOR]