Based on the combined sequences of mitochondrial Cytb and COI gene, the genetic diversity and population historical dynamics of Zacco platypus from the Sha River and the Juma River of the Baiyangdian Basin were analyzed. The results showed that 45 haplotypes were detected in 141 samples, and two of them were shared between the two populations. The haplotype diversity and nucleotide diversity of the Juma River (JMH) population (h=0.712 0, π=0.0118 2) were higher than those of the Sha River (SH) population (h=0.451 4, π=0.003 13). The analysis of molecular variance (AMOVA), genetic differentiation index (F_ST) and phylogenetic tree revealed that there was no obvious genetic differentiation between the two populations. The variation within the population (96.43%) was greater than that between the populations, and there was a large gene flow (6.745) between the two populations. Neutrality test and mismatch analysis showed that the SH population and the JMH population had not experienced population expansion. Bayesian skyline plot (BSP) indicated that the JMH population experienced population expansion before 0.004 million years, and the SH population remained stable. The effective population size of the Baiyangdian Basin experienced population expansion before 0.175 to 0.125 million years, and then remained stable. Combined with haplotype network and phylogenetic tree, the SH population has experienced the founder effect. According to the evolution rate of Cytb gene of Cyprinidae from 0.84% to 1.00% per million years, the divergence time of the two populations is estimated to be 0.089-0.067 million years ago.