This study analyzed the phylogeny, genetic diversity, and species identification of using the COI gene and 16S rRNA. Firstly, we obtained the complete mitochondrial genome of using Illumina sequencing. Compared with the mitochondrial genomes of the other close species, ATP8 was missing and tRNA^Met was duplicated in this genome. Based on the sequences of COI and 16S rRNA from the population, the nucleotide diversities of the COI gene and 16S rRNA were 0.00195 and 0.00073, respectively. The haplotype diversity of the COI gene was 0.76, larger than that of 16S rRNA (0.318). Secondly, a phylogenetic tree based on the mitochondrial proteins of species in Mactridae and Veneridae were constructed using the maximum likelihood (ML) method. Using this tree as a reference, we also constructed the ML phylogenetic trees using COI and 16S rRNA genes, respectively. These two trees were consistent with the reference, suggesting that these two DNA barcodes could be applied to the phylogenetic analysis. Thirdly, we analyzed the genetic distances based on sequences of the COI gene and 16S rRNA from 17 species in Mactridae and Veneridae. The average inter-and intra-species Kimura-2-parameter (K2P) distances based on COI sequences were 1.17 and 0.019, respectively. The average inter-and intra-species Kimura-2-parameter (K2P) distances based on 16S rRNA sequences were 1.117 and 0.018, respectively. The results suggested that for both the COI gene and 16S rRNA, the average inter-species genetic distances were 62 times larger than the intra-species distances. These results indicated that 16S rRNA could function as the COI gene to efficiently construct the phylogenetic tree and species identification. However, the COI gene could be used more effectively than 16S rRNA to analyze the genetic diversity of .