We analyzed and compared the polymorphism of mitochondrial COI gene sequence derived from three different groups of Babylonia areolata in Dongshan, Zhanjiang and Beihai by means of PCR. The results showed that the nucleotide sequence of COI gene was 680 bp with a high percentage of A+T base composition (about 62.42%); there were 32 singleton poylmorphic sites, 0.707±0.092 haplotype diversity, 0.001 85±0.000 39 nucleotide polymorphisms index, and 1.252 average number of nucleotide differences. Taking Babylonia lutosa and Nassarius as outgroups, we built NJ phylogenetic tree, its topology suggested that all the Babylonia areolata clustered together first, then mixed with Babylonia lutosa for one, and finally Nassarius formed independent.