Marine reserves have been identified as an important tool in the management of fishery resources and their number is increasing rapidly, most of them being on islands. However, knowledge on the real effect of protection from fishing on the genetic structure of populations, the spatial scales involved, or the suitability of islands as reserves in terms of connectivity, is scarce. This paper analyses the effects of fishery protection on the genetic structure of populations of Diplodus sargus, a target species, in protected and non-protected areas of the western Mediterranean. Populations studied showed high genetic variability at spatial scales from 101 to 103 km. Protected areas have significantly higher allelic richness. The lower levels of heterozygosis and higher heterozygote deficit showed by islands compared with coastal areas makes clear the importance of considering the connectivity processes when designing a MPA.