A new species of zoantharian within the genus Antipathozoanthus is described based on specimens collected from the coast of mainland Japan, northwest Pacific Ocean. Antipathozoanthus tubus sp. nov. is characterized by its substrate (epibiotic on polychaete tube) and habitat (exposed rock). As well, the results of molecular phylogenetic analyses using concatenated multiple genetic markers also support the distinction between A. tubus sp. nov. and its congenerics. Antipathozoanthus tubus sp. nov. is the first species of Antipathozoanthus species reported to be epibiotic on polychaete tubes, and is the second species in the genus that is not associated with antipatharians.