Habitat fragmentation in meadows of Posidonia oceanica, the most important and abundant seagrass in the Mediterranean Sea, was investigated at a region-wide spatial scale using a synthetic ecological index, the Patchiness Index (PI). We tested the hypothesis that human impacts are the major factor responsible for habitat fragmentation in P. oceanica meadows contrasting fragmentation of meadows located in “anthropized” areas with that of meadows located in areas with low anthropization and considered as virtually “natural”. We also related fragmentation of meadow with the morphodynamic state of the submerged beach (i.e. distinctive types of beach produced by the topography, the wave climate and the sediment composition) in order to investigate the influence of one natural component on the seagrass meadow seascape. Results demonstrated that fragmentation in the P. oceanica meadows is strongly influenced by the human component, being lower in natural meadows than in anthropized ones, and that it is little influenced by the morphodynamic state of the coast. The use of landscape approaches to discriminate natural disturbance from human impacts that affect seagrass meadows is thus recommended for the proper management of coastal zones.