Abstract: Natural resources of Barbatula toni have been seriously damaged in recent years due to habitat destruction and overfishing, which need urgent protection. The present study used mitochondrial DNA Cyt b and D-loop genes as molecular maker to perform the genetic diversity and phylogeographic analyses of three populations of B. toni from north China. 57 haplotypes were identified for 119 individuals of B. toni. No haplotype shared among different populations. Relatively high haplotype diversity (h=0.805—0.926) and low nucleotide diversity (π=0.00095—0.00458) were detected in three populations of B. toni. Haplotype Bayesian tree showed that B. toni from three river systems were separa-tely clustered as three clades. Analysis of molecular variance (AMOVA) indicated that the variation among populations (accounting for 79.45%) was the main source of variation. Differentiation index (F_ST) of three populations showed significant difference with F_ST >0.25 (P<0.01). Neutrality tests and mismatch distribution indicated the recent demographic expansion of B. toni. According to the average evolution rate of Cyt b of Cobitis melanoleuca from Siberia (0.68—0.84%/Ma), the divergence time of three populations of B. toni was 1.082—0.669 Ma, and recent demographic expansions time was at 0.071—0.047 Ma. Pleistocene climatic changes could be a key factor of the population dyna-mics.