, being distributed mainly in the upper reaches of Yellow River and lakes in the Qinghai-Tibetan Plateau, plays significant roles in the trophic web of plateau freshwater communities. In the present study, the complete sequences of the mitochondrial Cytb
gene (1 140 bp) from sixty eight individuals representing five populations from the upper Yellow River were obtained to assess the genetic variation and diversity. Within the aligned 1140 bp bases, 30 (2.63%) nucleotides were variable, and a total of 18 haplotypes were identified. The results showed that the haplotype diversity and nucleotide diversity of Gymncypris eckloni
populations were low by comparison with the other species of family Cyprinidae, which maybe related to tectonic movements and paleoenvironmental fluctuations of the Qinghai-Tibetan Plateau, and that the populations have experienced bottleneck events in history. The AMOVA analysis indicated that the genetic variation mainly occurred within populations instead of among different geographic groups or among populations within among different geographical groups. There is no geographic clustering observed in the phylogenetic tree and the TCS network, which suggest that the natural populations of Gymncypris eckloni
should be managed and conserved as a whole. The unimodal mismatch distribution of haplotypes, together with the selective neutrality test of Fu's Fs (−15.3400, P<0.001) and Tajima's D (−0.6254, P =0.3080), suggest that a recent population expansion of Gymncypris eckloni
have been occurred.