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The distribution patterns of loaches (Teleostei: Cobitoidea) were revealed in the River East Tiaoxi in China. Eight loach species (Cobitis sinensis, C. dolichorhynchus, C. laterimaculata, Misgurnus anguilicaudatus, Paramisgurnus dabryanus, Leptobotia tchangi, Vanmanenia pingchowensis and V. stenosoma) were found in field surveys at 90 sites. A macroscale analysis of the geographical distribution showed that related species were segregated in accordance with longitudinal alterations along the river course. M. anguillicaudatus was widely distributed from the middle reaches to upstream of the river whereas the related species, P. dabryanus, was distributed only downstream. Three spined loaches, namely C. dolichorhynchus, C. sinensis, and C. laterimaculata, were distributed in the middle reaches, the middle to upstream reaches, and the upstream section of the river, respectively. The distribution of V. pingchowensis was further upper stream than that of V. stenosoma in the upstream section. More detailed microscale analysis revealed that L. tchangi and the two Vanmanenia species, V. stenosoma and V. pingchowensis were mostly found in the ‘Riffle’ (lotic) habitats, whereas the two spined loaches, C. laterimaculata and C. sinensis preferred the ‘Pool’ (lentic) habitats. These results demonstrated that related loach species preferred similar habitat units in the River East Tiaoxi system.