Snakeheads are of important cultural value as ornamental fishes in China. In this study, the mitochondrial COI (cytochrome oxidase subunit I) gene fragments 576 bp long were used to analyze the phylogenetic and diversity of snakeheads in and out of China, to probe the probability of the COI gene to be used as a barcoding sequence for species identification. Including 149 specimens of different geographic populations of native to China, and 122 sequences of other species downloaded from GenBank, a total of 271 snakehead individuals of 25 species, were analyzed. Of all the sequences, no insertion-deletion sites existed. The average content of A+T (51.4%) was higher than that of G+C (48.6%). The average intraspecies genetic distance was 0.028, but reached 0.137 in , which was higher than some interspecies distances. The interspecies distances ranged from 0.030 to 0.302, with an average of 0.217. The largest distance exists between , exceeding some distances to outgroup. Phylogenetic trees based on the neighbor-joining and maximum likelihood method were constructed. Most individuals from the same species formed a monophyly, and high bootstrap values were obtained for them, but this was not the case for several other species. However, the relationships of species have low bootstrap values, indicating improper phylogenetic analysis of the COI gene for snakeheads. Furtherly, a compound were formed according to the phylogenetic trees. The results of this research indicate that the COI gene is proper for the species identification of native species of snakeheads in China, but more information regarding imported ornamental snakeheads is needed.