The population genetic approach delineates the species boundary of reproductively isolated corymbose acroporid corals

[Display omitted] ► To clarify the evolutionary process of Acropora species is difficult through molecular phylogenetic approaches. ► Phylogenetic analysis could not distinguish between Acropora digitifera and its cryptic species. ► Significant genetic differentiation was shown between these species by microsatellite markers. ► Their spawning seasons do not overlap, so interspecific hybridization could not occur. ► Population genetic analysis is quite informative to delimit the species boundary of Acropora species. In this study, we used a population genetic approach with microsatellite markers to attempt to clarify the species boundary of Acropora corals. Species in this taxon are usually difficult to distinguish with the usual molecular phylogenetic approach. We used Acropora sp. 1 and Acropora digitifera as the target species to shed light on the species boundary of Acropora at the population level. These species are morphologically and ecologically similar but are reproductively isolated by differences of a few months in their spawning seasons. We could not distinguish these species using a phylogenetic analysis of the mitochondrial control region, as previously reported in other Acropora species. In contrast, a population genetic approach clearly distinguished these species both sympatrically and allopatrically. Our results suggest that recent speciation and shared ancestral polymorphisms could partly explain the para- and polyphyly of several Acropora species.