The ecological structure of Posidonia oceanica (L.) Delile meadows was evaluated on the northern coast of Lazio, Italy (central Tyrrhenian, Mediterranean sea). This is an infra-littoral zone with a wide range of anthropogenic activities and high geo-morphological variability, which reflects heterogeneity in shoot density, leaf morphology and biomass in fragmented patches. Genetic variability in populations corresponds to the formation of 3 sub-clusters, in the diverse impacted zones (north, centre and south), being correlated to the geographical distance between sites. AMOVA estimated a high genetic variation showing 43.05% individual differences within populations with a marked differentiation among the populations (56.9%) indicated by Fst value (0.57). These results revealed the role of the genetic structure of seagrasses for determining selectivity of fragmented habitat, in response to natural drivers. They showed that site-specific self-recruitment is related to biodiversity capacity and to the geo-morphological characteristic of the coast.