No clear method of identifying species in the zoanthid genus Zoanthus has been established, due in part to the morphological plasticity of this genus (e.g., in polyp and colony form, oral disk color, tentacle number). Previous research utilizing the mitochondrial cytochrome oxidase I gene (COI) as a phylogenetic marker indicated that Zoanthus spp. in Japan may consist of only one or two species, despite a bewildering variety of observed morphotypes. Here we have utilized not only COI but also mitochondrial 16S ribosomal DNA (mt 16S rDNA) in order to clarify the extent of Zoanthus species diversity in southern Japan. Our molecular genetic results clearly show the presence of three monophyletic Zoanthus species groups with varying levels of morphological plasticity, including the new species Z. gigantus n. sp. and Z. kuroshio n. sp. We describe all three species found in this study, and identify potential morphological characters (coenenchyme and polyp structure as well as polyp external surface pigmentation patterns) useful in Zoanthus species identification. A morphological dichotomous key is provided to assist in field species identification.

Recent investigations into the encrusting anemone genus Zoanthus using molecular and morphological techniques have begun to bring order to this taxonomically neglected group. Previous studies have confirmed the existence of three distinct species present in southern Japan: Z. sansibaricus, Z. kuroshio, and Z. gigantus. Results from such studies show species of Zoanthus to be highly morphologically plastic, often incorporating morphotypes with varying oral disk color and oral disk diameter. Literature lists the species Z. aff. vietnamensis as occurring in southern Japan and throughout the western Pacific Ocean, but due to the morphological plasticity of Zoanthus species, a re-examination of Z. aff. vietnamensis using molecular techniques was needed. Here, using mitochondrial 16S rDNA and the nuclear internal transcribed spacer of ribosomal DNA (ITS-rDNA) sequences, as well as morphological data, we have examined several nominal Z. aff. vietnamensis samples collected from Kagoshima Bay and Yakushima Island, Japan. Based on polyp length and diameter, oral disk diameter, mesentery and tentacle numbers, and colony form, Z. aff. vietnamensis is easily distinguishable from Z. sansibaricus, Z. kuroshio, and Z. gigantus. However, despite these clear morphological differences, our mitochondrial and nuclear sequence-based phylogenies indicate that Z. aff. vietnamensis and Z. kuroshio are very closely related (perhaps conspecific), highlighting the morphological plasticity of this genus and the difficulty of species identification based on morphological data alone.