The distribution of the loach Paracobitis variegatus is confined to upper Yangze, ZHuanghe and Nanpanjiang drainages. The nember of branched dorsal fin rays, morphology of anterior nostril, colour pattern of head and the length of maxillary barbel indicate that it has differentiated into two subspecies. Both subspecies are isolated geographically: P.variegatus variegatus restricted to the upper Yangze and the upper Huanghe Rivers, and P.variegatus longidorsalis, new subspecies, to the upper Nanpanjiang River. The subspecific differentiation is supposed to correlated to the sharp uplift of the eastern Yunnan Plateau during late Pleistocene. The taxonomic status of Nemachilus berezowskii Gunther, 1896 and Nemacheilus oxygnathus Regan, 1908 are also discussed and they are considered to be the synonyms of P.variegatus variegatus.