To investigate the impact of potential marine barriers on gene-flow in high dispersal marine invertebrates, we assessed the population genetic structure of the sea star Astropecten aranciacus. Samples were obtained from nine locations within the Atlantic and the Mediterranean Sea including populations east of the Siculo-Tunisian Strait. We obtained both DNA sequence data of the mitochondrial control region and genotype data at four microsatellite loci. Both markers were highly polymorphic and showed a great level of genetic diversity. Genetic differentiation between populations (F (ST)) was in general low, particularly for nuclear data, as is often the case in high dispersal marine invertebrates. Nevertheless, both marker sets indicated a significant genetic differentiation of the population from the island of Madeira to most other populations. Our results also demonstrate a clear pattern of isolation-by-distance supported by both mitochondrial and nuclear markers. Therefore, we conclude that larval dispersal of A. aranciacus is somewhat limited even within the basins of the Atlantic, the west Mediterranean and the east Mediterranean. Microsatellite loci further revealed genetic differentiation between the three basins; however, it is not clear whether this is truly caused by marine barriers. Genetic differentiation between basins might also be a result of isolation-by-distance allowing for any grouping to be significant as long as geographical neighbors are clustered together. Although levels of genetic differentiation were less pronounced in mirosatellite data, both datasets were coherent and revealed similar patterns of genetic structure in A. aranciacus.