The aim of this study was to explore the genetic variation characteristics and the level of genetic variation of Sinipercine fishes in the National Aquatic Germplasm Resources Protection Area of Jinjiang River. Based on PCR amplification and sequencing technologies, the mitochondrial control region (D-loop) sequences of Siniperca kneri, Siniperca scherzeri, Coreoperca whiteheadi(3 groups, 97 fish)were compared and analyzed. The results showed that:the sequence length of Siniperca kneri was 843 bp with no variation sites and 1 haplotype was identified; The Coreoperca whiteheadi length sequence had two types of 852 bp and 856 bp, and 28 polymorphic loci and 11 unique haplotypes were identified; The length sequences of Siniperca scherzeri were 845 bp and 846 bp with 5 polymorphic loci and 5 haplotypes were identified. The genetic distance were 0.000 0, 0.002 0±0.000 9 and 0.008 7±0.002 0 in the three groups; The haplotype diversity and nucleotide polymorphism were 0.000 0, 0.859 9, 0.7367 and 0.000 0, 0.008 7, 0.002 0, respectively. The experiment and analysis indicated that there were differences among the termination sequence regions and the conserved sequence regions. For the three populations, Coreoperca whiteheadi was a stable population with great genetic variation and rich diversity. Due to bottleneck effect, although the Siniperca scherzeri had rich haplotype diversity, but had low nucleotide diversity; Siniperca kneri had single hereditary composition, and diversity was very poor. Presumably, there may be a invasive breeding population. Jinjiang, as the biggest river of Fanjing Mountain National Nature Reserve area, once with rich resources of the Sinipercine, but had been badly damaged. It is necessary to strengthen the research and protection of the genetic resources.