A survey of genomic DNA from the polychaete Chaetopterus variopedatus was conducted using the polymerase chain reaction. Twelve unique homeobox-containing gene fragments were recovered. Phylogenetic analysis indicates that seven of the fragments are from genes belonging to Hox homeobox classes. Other fragments show orthology with Xlox, caudal, and Prh homeobox classes, with two fragments not definitely assignable to a homeobox class by our analysis. Orthology with gene sequences reported for the polychaete Ctenodrilus serratus, by Dick and Buss (1994), was calculated and indicated that at least eight of the C. variopedatus fragments are homologous to these previously reported sequences. Tabulation of the Hox gene relationships suggest that polychaetes have representative genes of each of the Hox cognate groups except Abd-B. This conclusion further suggests that the Hox cluster in the basal protostome ancestor had already undergone the gene duplications leading to the complete complement of homeotic genes known in Drosophila, with the possible loss of Abd-B in the polychaete lineage.