We explore the phylogeography of the broadcast spawner Marthasterias glacialis along south Europe and Azores. Sequences of the cytochrome c oxidase gene from 225 specimens, belonging to 10 localities, were analysed. We found 73 haplotypes grouped within two lineages (divergence 2.9%). One lineage was AtlantoMediterranean, whereas another one was exclusively Mediterranean. Estimation of lineages split goes back to 830,000-580,000 (±120,000) years ago. This suggests that sea-level oscillations during the Pleistocene glaciations promoted gene flow interruption, lineage divergence between basins and cryptic speciation. Secondary contact between populations allowed a recolonization of the Mediterranean by the Atlantic lineage. When animals of the Atlanto-Mediterranean lineage were considered separately, F st index and AMOVA did not show significant differences between populations along either the Iberian Peninsula or basins. Isolation by distance between populations was not detected, and only populations of Plymouth and Azores showed significant differences to all the others.The remoteness of Azores islands might explain the structure of this population. Haphazard arrival of larvae and local extinctions rather than contemporary restricted gene flow might be responsible for the distinctive population structure of Plymouth.