Molluscs belong to one of the two protostome superphyla, the Lophotrochozoa. Among molluscs, bivalves show a characteristic shell morphology separated bilaterally into two plates. The connection between the modification of the development and evolution of the molluscan body plan can be study identifying and obtaining information on the genes that regulate the development of bivalves. Homeobox genes are involved in body plan formation and in the regulation of many developmental processes in bilateria. For this reason, the evolutionary history of Hox, ParaHox, EHGbox, and NK homeobox gene families could be crucial to understand the evolution of molluscan body plans and phylogeny. The aim of this work was to compare these genes from different Bivalvia families. In this study, 22 homeobox gene fragments from five bivalve species were identified, and then these homeodomain sequences were compared with those available from other bivalves. The Hox cluster in bivalve molluscs has 11 genes. Regarding the ParaHox cluster, current data suggest that the ParaHox genes are also conserved in bivalves. Two EHGbox genes are well conserved in bivalves (en and Gbx); however, there are no data about the presence of the third one (Mnx). The NK cluster has not been examined in depth in Bivalvia; however, the conservation of Tlx and NK2 genes in different species can be confirmed. The study of the genes reported here might contribute to the understanding of their evolutionary history within the phylum and the involvement of these genes in the body plan of bivalves.