Liobagrus nigricauda is endemic to the upper Yangtze River basin. By using the fast isolation by amplified fragment polymorphism of sequences containing cytochrome b, we identified the genetic variation in 6 populations of L. nigricauda. A total 21 nucleotide sites were detected in 1086 bps from cytochrome b, and 16 haplotypes were defined from 145 sequences. Nucleotide diversity index was 0.00087, and haplotype diversity index was 0.26858. Hierarchical Analysis of Molecular Variance (AMOVA) showed that the variation on within populations was 93.03%. And the mainstream populations of the upper Yangtze River had preliminary genetic differentiation with the tributary.
