The genus Protothaca (Bivalvia: Veneridae) represents a commercially important group of clams with a widedistribution in the Pacific coast of America and Asia. According to The Integrated Taxonomic Information System (ITIS),there are nine accepted species (http://www.itis.gov/); nevertheless the number of recognized species varies based on thesources revised. In this study, a molecular approach was used to phylogenetically analyze five species belonging to the genusProtothaca. A fragment of 550 bp from the mitochondrial cytochrome oxidase I gene was analyzed from P. asperrima, P.columbiensis, P. grata, P. mcgyntyi and P. jedoensis. The COI sequences revealed seven haplotypes for P. asperrima, four forP. columbiensis and two for P. grata. Bayesian analysis showed two major well supported clusters consisting of (1) genus-Protothaca clade and (2) a clade with rest of the members of Veneridae. All the species of Protothaca clustered together withthe exception of P. jedoensis. Intraspecific genetic differences in P. asperrima were very high at 17-18 %; P. columbiensisand P. grata specimens had differences in the range of 0,18-0.36 % and 0,92 % respectively. Interestingly, Protothacaasperrima haplotypes A and H showed the highest level of intraspecific genetic distances. Considering the traditionalcontroversies in classification, the level of COI divergence in P. asperrima haplotypes and the differences observed in othergenera within the family Veneridae, we propose a revision of the species including elevating the rank of the two distinctclusters of P. asperrima to closely related species status.