Sequence analysis based on the mitochondrial cytochrome c oxidase subunit I (COI) gene fragment was conducted for 21 clam species belonging to the family Veneridae to determine the utility of this sequence in identifying phylogeographic and phylogenetic structure. The DNAs of 21 clam species were extracted and subjected to PCR using primers COI-F and COI-R. The resultant COI fragment was 707 bp in all species, with A+T contents ranging from 62.4%-67.8%. The COI gene sequences of all 21 species were analyzed using MEGA 5.0 software. Interspecific COI sequence divergences was very high, ranging from 7.2%-38.2%, mainly as a result of transitions and transversions. The minimum value of 7.2% was observed between Meretrix meretrix and Meretrix lusoria, and the maximum value of 38.2% was between Tapes literata and Cyclina sinensis. M. lusoria exhibited 0.4% intraspecific sequence divergence among three sequenced individuals. However, for other species, the COI sequences were identical among the three sequenced individuals for each species. An analysis of COI gene sequence variation among 21 species revealed 379 variable sites, of which 334 were parsimony-informative sites, with 72 transitions (si) and 93 transversions (sv) (si/sv=0.8). Meanwhile, no indels (insertions/deletions) were detected in the COI sequences from any samples. The percentage of interspecific sequence divergence within the same genus, intergeneric sequence divergence within the same subfamily, and those between subfamilies were analyzed. The mean values were 12.5%-27.3%, 19.7%-29.0% and 29.2%, respectively. The COI fragment encodes 235 amino acids, of which 100 sites were variable. A phylogenetic tree of 35 Veneridae clams was constructed based on the COI nucleotide sequences, with Mactra chinensis as an outgroup species. Tree topologies showed that all species of Veneridae are in the same group, forming a clade distinct from the outgroup species. Within Veneridae, six species of the subfamily Dosininae formed a clade with a bootstrap value of 75%. Two species of the subfamily Venerinae formed another clade with a bootstrap value of 93%. All species of the subfamily Meretricinae formed a monophyletic group with a bootstrap value of 70%, in which M. meretrix, M. lusoria and Meretrix petechialis were first clustered with a high bootstrap value of 99%. This result indicated that M. meretrix, M. lusoria, and M. petechialis have a closer relationship than other species. An analysis of tree topology and sequence alignment indicated that M. lusoria, M. petechialis, and M. meretrix are closely related species. The data support the viewpoint that M. petechialis and M. lusoria should be treated as synonymous with M. meretrix, and may be described as two geographical subspecies. The data also support the perspective that Dosinia corrugata and Dosinia angulosa are two distinct species. The validity of Paphia undulata and Paphia textile as different species is also supported. This result reveals that the COI gene is an appropriate marker for studies in phylogeny and phylogeography of the Veneridae clams.