The seagrass Cymodocea nodosa forms a unique community in the Canary Islands, where it is classified as an endangered species. Biogeographic theory predicts that clonal species on islands near their distributional limits might show lower proportions of sexual (versus clonal) reproduction, lower genetic diversity, and higher differentiation. We addressed these hypotheses by comparing the genetic structure of C. nodosa from 10 meadows in the 4 main Canary Islands with 2 Iberian sites (Atlantic and Mediterranean) using microsatellites. A resampling method was proposed to standardize, among samples, genetic variability statistics estimating genotypic richness (R) and allelic richness (A). A high degree of genotypic richness at the Canary Islands (R = 0.30 - 0.94, mean = 0.67) relative to Iberian sites revealed that C. nodosa performs effective sexual reproduction here. In contrast, lower A suggested a founder effect during the colonization of the archipelago, and similar allelic composition across all islands indicated colonization from a single source. A hotspot of genetic diversity was observed in El Medano (Tenerife), probably associated with lower drift in this meadow, the largest of the archipelago. Predominant north-south surface currents and a greater distance to the mainland could explain lower allelic richness of 2 northwestern sites on different islands and greater similarity between them. All meadows were differentiated from each other and there was no correlation between genetic and geographic distances. This non-equilibrium migration-mutation system was therefore mostly influenced by diversity resulting from genetic drift, and less by the homogenizing effects of gene flow.