Perca fluviatilis (Perca), which belongs to the Perciformes order and Percidae family, and commonly known as Eurasian perch, is a precious species of freshwater fish favored for its delicious meat, high nutritional value, short growth period, and strong disease resistance. Perca fluviatilis is widely distributed in Europe and North Asia. To determine the genetic status of Perca fluviatilis in Xinjiang, the genetic diversity of four Perca fluviatilis populations in the Wulungu River and Kalaeerqisi River in Xinjiang was analyzed using mitochondrial CO I, Cyt b, and D-loop sequences, and then compared with that of the European populations. The CO I, Cyt b, and D-loop sequences of the four populations in Xinjiang had 3, 10, and 10 variable sites, respectively (accounting for 0.49%, 0.90%, and 1.92%, respectively, of the total sequence length), which defined 4, 11, and 11 haplotypes, respectively. Further, the haplotype diversity was 0.065±0.022, 0.276±0.049, and 0.186±0.046, respectively, and the nucleotide diversity was 0.00011±0.00004, 0.00033±0.00007, and 0.00084±0.00013, respectively, indicating low genetic diversity. No shared haplotype was found between the Chinese Xinjiang and European Perca fluviatilis populations. Further, the haplotype cluster tree and network diagram revealed obvious separation, thereby indicating different genetic pedigrees. Based on the Cyt b and D-loop sequences, the estimated variation among the populations of Wulungu Lake (WL), Jili Lake (JH), and Wulungu River (WR) in the Wulungu River basin in Xinjiang, China, was ?0.005% and 0.44%, respectively, and the coefficient of genetic differentiation (F_st) was ?0.00045 and 0.00436, indicating a low degree of differentiation (F_st＜0.05). Of note, the F_st between any population was low (F_st: ?0.01158?0.01803), indicating frequent genetic communication and the same genetic pedigree. In particular, shared haplotypes were identified between the two lakes, with a negative F_st and frequent gene exchanges with no genetic differentiation. Based on the CO I gene, the four populations of Kalaeerqisi (ER) and WR, WL, and JH were estimated to vary by 1.57% among the populations, with an F_st of 0.01568. However, the ER population and WL population had a moderate genetic differentiation (F_st=0.06614＞0.05), while the ER and WR populations had a high genetic differentiation (F_st=0.24627＞0.15). The replenishing of genetic resources may not occur due to the blockage of the dam. Further, the Kalaeerqisi River formed an independent genetic pedigree. Overall, these findings serve as a reference for the diversity of Xinjiang Perca fluviatilis populations and the development and utilization of germplasm resources.