Coastal urbanization and the consequent proliferation of artificial structures greatly impact rocky reef communities, productive and diverse marine environments that play a crucial role in the functioning of broader coastal ecosystems. This study, conducted along a 7 km stretch of coastline at increasing distance from the port of Genoa (Ligurian Sea), investigated whether the alternating presence of artificial and natural reefs leads to discernible differences in the biota inhabiting these two reef types. The study area is one of the most anthropized areas of the Mediterranean Sea, exhibiting nearly 60% coastal artificialization, which severely impacts coastal ecosystems, favouring the replacement of sensitive species with more tolerant species. Ten reefs (5 natural and 5 artificial) were surveyed by scuba diving at about a 6-m depth, employing quadrats of 50 cm × 50 cm to estimate visually the percent cover of conspicuous sessile organisms. The artificial reefs hosted a similar number of species (18) to their natural counterparts (19) but exhibited a distinct community composition: the former were especially characterized by Jania rubens and filamentous algae, with the latter characterized by Peyssonnelia squamaria and Mesophyllum lichenoides. This difference, however, became negligible where coastal habitat fragmentation (here measured with a purposely devised Fragmentation Index) was minimal. Reducing fragmentation may therefore represent a management strategy to minimize the potential impact of artificial structures on marine biodiversity.