The population genetics of Patella ferruginea Gmelin, 1791, an endangered limpet endemic to the western Mediterranean, has been analysed using 11 polymorphic microsatellite markers on 533 individuals from 18 localities throughout its distribution area. The results showed a deficit of heterozygotes, denoting a certain degree of inbreeding, and, with an overall FST of 0.004, a low level of genetic variability among localities. These data indicate that the species is distributed as a metapopulation (an assemblage of discrete local populations with migration among them) along most of the species’ range. Moreover, 99% of the variability observed was within populations, with only 0.41% accounting for between-population variability. No pattern of isolation-by-distance was found, and 35.5% of the individuals were recognised as migrants. Altogether, the findings indicate that most of the populations studied are connected to each other to some extent and that larvae of the species show a higher dispersal capacity than previously assumed. The exchange network does not follow a clear direction but rather shows a chaotic pattern attributed to stochastic factors resulting from the complex interaction of biotic and abiotic factors. This pattern indicates the lack of strong barriers to dispersal in the study area and permeable barriers that do not limit population connectivity. A relatively high level of self-recruitment and occasional stochastic dispersal events at variable distances are also evidenced by the analyses. Currently, marine protected areas (MPAs) safeguard the benthic adults but not the larval phase of the species. Considering our results, the conservation of P. ferruginea should be based on a holistic approach in which the protection of its habitats extends from the benthic to the pelagic zones, which will help maintain the larval pool and promote larval dispersal and settlement and, ultimately, gene flow. Lastly, conservation efforts must prioritise the survival of the extant populations of P. ferruginea, both within and outside MPAs, over measures that require the manipulation or translocation of specimens.