DNA barcoding has been widely used in the fields of taxonomy, identification, phylogenetic evolution, and population genetic analysis of marine shellfish. To further evaluate the identification validity of different DNA barcoding genes in marine shellfish, sequences of COI, 16S rRNA, 18S rRNA, and 28S rRNA from Veneroida were randomly downloaded from the GenBank database, analyzed by the distance-and tree-based methods, and taxonomic relation established by the tree-based method, and compared the results with some sequences from our laboratory. According to the "10×rule" and "2%" standard criterion, 57.1% of species could be distinguished using the COI gene, whereas 16S rRNA identified 60.9%, 18S rRNA identified 16.7%, and 28S rRNA did not identify any species. We also found that there were significant barcode gaps between the genetic distances of pairwise-and within-species in most genera based on COI and 16S rRNA genes; however, there were significant overlaps, instead of barcode gaps, based on 18S rRNA and 28S rRNA. The cluster analysis showed that 87.9% of individuals clustered to a monophyletic group, with other within-species individuals clustered on the COI; and 65.6% 16S rRNA individuals clustered in monophyletic groups. Furthermore individuals without monophyletic groups clustered into sister groups, which revealed that the evolutionary relationships showed by the NJ tree constructed via COI and 16S rRNA mainly agreed with that from the morphological classification, especially that of the COI gene. In contrast, the NJ tree constructed via 18S rRNA and 28S rRNA genes showed disordered clustering relationships, including some individuals from different species cluster to monophyletic groups. In the present study, the results clearly suggested that both COI and 16S rRNA can be used as DNA barcodes in identifying species in Veneroida, particular COI, but 18S rRNA and 28S rRNA are not suitable because of the large intraspecific variation. This study provides new data for DNA barcode selection in Veneroida.