Hox genes have pivotal roles in animal body plan formation. We identified Hox genes and inferred the organizations of the Hox gene hypothetical ancestral cluster by a polymerase chain reaction (PCR) survey for the phylum Mollusca, so as to assess possible correlations with morphological diversity. All the extant classes, except for Monoplacophora, were examined, namely Solenogastres, Caudofoveata, Polyplacophora, Cephalopoda, Gastropoda, Scaphopoda, and Bivalvia. The result showed that the molluscs primarily possessed anterior, medial and posterior cognates of the Hox genes, ParaHox genes (Gsx, Xlox, and Cdx homologues), as well as non-Hox/ParaHox type homeobox genes (Gbx and Msx homologues). The last common ancestor of molluscs is inferred to have had twelve Hox genes: three anterior, seven medial and two posterior cognates. These results suggest that some of the anterior or posterior cognates have been lost in some lineages, most notably in Caudofoveata, while the medial cognates showed both losses and duplications. One of the medial cognates was found to be duplicated in all the classes examined except for Gastropoda, but not in other Metazoa, suggesting that this feature could be a synapomorphy of molluscs.