Compared with other diploid teleosts (2n=48), anguilloid fish have a specialized karyotype (2n=38) and remarkable morphological variation, and represent one basal group species of teleosts. To investigate the Hox gene/cluster inventory in basal teleosts, a PCR-based survey of Hox genes in the Japanese eel (Anguilla japonica) was conducted with both gene-specific and homeobox-targeted degenerate primers. Our data provide evidence that at least 34 distinct Hox genes exist in the Japanese eel genome and that they represent eight Hox clusters. Duplication of Hox genes in the Japanese eel appears to be the result of the fish-specific genome duplication (FSGD) event. The Japanese eel shared the FSGD event with other teleosts such as zebrafish and pufferfish. A member of Hox paralog group one (HoxA1b) was preserved in the Japanese eel but was lost in other teleosts. Available Hox data revealed that the Hox cluster evolved distinctly in different teleost lineages. All duplicated Hox clusters were retained after the FSGD event in basal teleosts like in the Japanese eel, whereas crown teleosts lost one cluster (HoxCb or HoxDb). Based on current teleostean phylogeny, the HoxDb cluster was lost independently in the teleost lineages Otocephala and Euteleostei.