The seastar Ophidiaster ophidianus is a vulnerable and protected species in the Mediterranean Sea but is common on North Atlantic islands such as the Azores and Madeira archipelagos. This work presents new insights into the phylogeography and genetic diversity of O. ophidianus from the Azores, based on 67 sequences of the 16S mitochondrial gene and 46 sequences of the nuclear ATP intron 5 gene. Twenty-six samples from the Mediterranean and seven samples from Madeira were used as out-groups. The results revealed that there is a lack of genetic differentiation between O. ophidianus from the Azores and the out-groups. All, therefore, belong to the same lineage and argue for a fast and recent range expansion of this species into the Azores. Our results also suggest the existence of distinctive periods of strong gene flow followed by periods of either low or non-existent gene flow between the Mediterranean Sea and this archipelago, which could explain the presence of private haplotypes in all studied areas.