The present study aims at a phylogeographic description of Zacco platypus from southeast China, in order to detect subdivisions within the nominal species. Two main basins were sampled: the Chang Jiang (Yangstze River) in central and east China (Hunan and Sichuan provinces) and the Xi Jiang, the more southern main tributary of the Zhu Jiang (Pearl River, Guangxi province). A total of 27 intron systems were tested, five of them were informative and gave 12 interpretable and polymorphic loci. Within the diversity of Z. platypus, four genetic groups were identified by multidimensional (FCA) analyses, corresponding to distinct genetic pools. The geographical distribution of the genetic groups corresponds neither with the drainage structure, nor the geographic distances between samples. It follows that isolation by distance and limited migration are insufficient to explain this geographic structure. The history of the river network therefore appears to have played an important role.