Pomacea canaliculata and P. maculata have similar morphological characteristics. They are the two most common and highly invasive apple snail species, which seriously damage crops and aquatic ecosystem in China. The present study identified the species and analyzed the genetic diversity of 40 samples of Pomacea spp. from five sampling sites in Suzhou city, Jiangsu Province, based on their mitochondrial cytochrome I oxidase subunit (COI) and nuclear gene (EF1α) sequences. Some genetic diversity parameters were analyzed by DnaSP 5.0, and the base composition, the number of nucleic site replacement were analyzed by MEGA 7.0. A Bayesian phylogenetic tree was constructed using PhyloSuite. The results showed that a total of 40 mitochondrial COI gene sequences with a length of 605 bp were obtained in 40 samples, and a total of 74 variable sites and 4 haplotypes were detected among all sequences (Table 1). The 34 samples in Suzhou were P. canaliculata, and the other 6 samples were P. maculata. Among them, three haplotypes (PcaH1﹣PcaH3) were found in P. canaliculata and one haplotype (PmaH1) was found in P. maculata (Table 1). The haplotype diversity (h) and nucleotide diversity (π) of P. canaliculata were 0.399 and 0.017, respectively. Only one haplotype was found in P. maculata. Compared with other invasive areas of China, the genetic diversity of P. canaliculata and P. maculata from Suzhou city were low. Based on the phylogenetic relationship of mitochondrial COI gene, it was suggested that P. canaliculata probably traced back to Argentina, while P. maculata in Suzhou city were probably originated from Brazil. In addition, Zhoushi town in Kunshan city was a newly discovered sympatric distribution area of these two species. Based on nuclear gene (EF1α) sequences, 28 nuclear gene (EF1α) sequences with a length of 430 bp were obtained in 9 samples selected from Suzhou City and Kunshan City after cycle sequencing. A total of 40 variable sites and 9 haplotypes (EFHAP1﹣EFHAP9) were detected among all sequences (Table 1). Eight haplotypes (EFHAP1﹣EFHAP5, EFHAP7﹣EFHAP9) were found in P. canaliculata and two haplotypes (EFHAP5 and EFHAP6) were found in P. maculata (Table 1). Phylogenetic tree analysis based on mitochondrial COI gene and nuclear EF1α gene suggested that there was genetic exchange between P. canaliculata and P. maculata (Fig. 1 and Fig. 2), indicating that hybridization between P. canaliculata and P. maculata exists.