The role of habitat degradation on the spread of the alien green alga Caulerpa cylindracea is reported here by comparing observations achieved through a multi-year assessment on three Mediterraneans habitats, namely Posidonia oceanica meadows, Phyllophora crispa turf, and coralligenous reefs. Due to the peculiarity of the study site, both natural-reference and impacted conditions were investigated. C. cylindracea occurred in all the studied habitats under impacted conditions. High susceptibility to the invasion characterized impacted P. oceanica, where Caulerpa cover reached 70.0% in summer months. C. cylindracea cover did not differ significantly among conditions in P. crispa turf, where values never exceeded 5.0%. Conversely, the invasive green algae was low in abundance and patchily distributed in coralligenous reefs. Our results confirmed that habitat loss enhances the spread of C. cylindracea, although with different magnitudes among habitats. Dead matte areas of P. oceanica represented the most vulnerable habitat among those analyzed, whereas coralligenous reefs were less susceptible to the invasion under both the studied conditions.