Due to the dearth of molecular markers variable enough to distinguish species of black corals, species delimitation in Antipatharia is still mainly based on morphological traits. One of the few markers available, the internal transcribed spacer (ITS) region located in ribosomal DNA, has already been used several times to infer phylogenetic relationships among antipatharians. However, this region was never considered in population-scale studies of shallow-water black corals till now. Here, we sampled two phenotypic variants of 41 specimens of the shallow-water antipatharian Stichopathes cf. maldivensis along the SW of Madagascar. The sampling area represents 200 km of shore and encompasses the runoffs of three rivers. We used direct sequencing to determine the main ITS1 types present in the genomes of the collected specimens and retrieved sequences from GenBank for Indonesian specimens. Then, we constructed a haploweb to visualize possible species boundaries using the criterion of mutual allelic exclusivity. With this method, we confirm that the previously described phenotypic variants belong to a single species that apparently extends from Indonesia to Madagascar. Likewise, the three rivers that pour freshwater in southwestern Madagascar do not appear to act as a barrier for the larval dispersal of this species. This study highlights the usefulness of ITS markers within antipatharians at both species and population levels.
