Limpet harvesting in Azores (NE Atlantic) has been taking place probably since the islands were first colonized in the XV century. Limpet species are highly exploited and populations from most islands have declined steadily bringing about catastrophic effects on coastal communities. Despite their economic importance limpets are also ecologically key species and require prioritizing conservation strategies. Patellid limpets are broadcast spawners which go through a planktonic larval stage in their life cycle. They are benthic as adults and the larva is the only phase during their life-cycle which has the ability to disperse over assumed large spatial distances. However, there is now mounting evidence that gene flow between islands and mainlands can be low, even for species with a relatively long planktonic larval stage. Low levels of larval exchange may thus limit the success of conservation objectives expected upon migration and recruitment. In dispersive isolated oceanic islands such as the Macaronesian Islands, the Azores Archipelago in particular, is not clear whether limpet populations from different islands form a single meta-population or, in contrast, populations on each island are isolated from the rest. Knowledge on this scenario is crucial for the management and conservation of exploited populations of limpets. Here we have developed and described species-specific multiplexed microsatellite markers for the limpet Patella aspera using whole genome shotgun 454 sequencing. These genetic tools can allow the study of the population genetic structure and evolutionary history of patellid species in the archipelago of Azores. Genetic studies, alongside with biological, ecological and oceanographic information, represent an important contribution for the understanding of population dynamics by allowing testing hypothesis about larval dispersal patterns, recruitment and life history traits, population connectivity, genetic diversity, and population equilibrium.