In this study we assessed the sequence variation in the I3-M11 partition of the mtDNA cytochrome c oxidase subunit I gene (COI) in ten populations of the Atlanto-Mediterranean demosponge Phorbas fictitius (Porifera: Poecilosclerida) at two spatial scales: a regional scale comparing mainland (Iberian) and insular (Macaronesian) populations, and a local (Archipelagic) scale focusing on different island populations of the Azores archipelago. A multiple approach combining diversity measures, FST estimates, phylogenetic inference and nested clade phylogeographic analysis was used to assess the genetic structure and elucidate the evolutionary history of this species. Genetic differentiation, based of FST estimates, was found among most populations at both scales revealing highly structured populations. This results of a presumably low dispersal potential and bathymetric range of the species, and the geographical isolation of the studied populations. However we found evidence of long distance dispersal events between some populations. Phylogenetic and network analyses indicate a separation of insular (Macaronesian) and mainland (Iberian) clades with only two haplotypes shared between these areas. The high genetic diversity and prevalence of ancestral haplotypes suggest the Macaronesian islands as the likely place of origin of this species with posterior expansion to mainland locations via current-mediated dispersal of larvae or sponge fragments. This study adds to the growing evidence of structured populations in the marine realm and highlights the importance of the Macaronesian islands on the evolutionary history of the Northeast Atlantic marine biota.