Abstract: The complete mtDNA cytochrome b gene sequence (1141bp) was sequenced for 16 Schizopygopsis from the upper reach of the Yellow River and the Tuosuo Lake of the QaidamBasin.The sequence compositions and variations were analyzed using MEGA2.1 software.The Gymnocypris przewalskii and Gymnocypris eckloni and Platypharodon extremus were selected as outgroup,and one molecular phylogenetic tree of 5 haplotypes was constructed using NJ in PAPU 34.0b10 software.The monophyly of the populations of the Schizopygopsis from either the Yellow River or the Tuosuo Lake was not supported.The genetic variability (Fst) and the value of exact test of differentiation between the populations calculated with Arlequin Ver.2000 software were 01204(P0105) and 0.0532 (P0105), respectively.The Nm value deduced from Fst between the populations was 1195.These data suggested that the populations of the Schizopygopsis from the Yellow River and the Tuosuo Lake have not evolved to two different species.Our results support the morphological classification that merging the Schizopygopsis kessleri into Schizopygopsis pylzovi.The nucleotide diversity () exhibited by two populations was low (010012～010026).Inferred from the molecular evolution rate,the divergent time of the S.pylozovi from the Yellow River and the Tuosuo Lake was about 70000 years ago in the late Pleistocene.The faunal connection for population of the in historical was analyzed according to the phylogeography of population distributions and paleo2geographical events.