The Pelagos Sanctuary hosts eight resident cetacean species. Genetically different from Atlantic populations, their conservation is essential to preserve the whole biodiversity of the Ligurian Sea. The NATURA 2000 network is currently identified as one of the most efficient conservation tools due to its legally binding nature; however, its effectiveness for cetacean preservation is still unclear. The study used data systematically collected within the Pelagos Sanctuary from 2008 to 2021 by the FLT Med Net and the LIFE Conceptu Maris projects to investigate cetaceans distribution, Richness and diversity related to the existing protected areas. Of the 423 hexagons considered, only 21.28% of the study area was covered by French NATURA 2000 sites and 9.22% by Italian sites. French NATURA 2000 sites had the highest coverage of weighted Encounter Rate (ER_w) and biodiversity values. Only three species showed statistically significant differences between the French and Italian protected and non-protected hexagons, and biodiversity showed no significant difference. Only T. truncatus had higher median over Italian protected hexagons. The Pelagos Sanctuary still lacks offshore NATURA 2000 sites, especially in Italian waters. For this reason, areas to amplify the Network aimed at increasing cetacean and biodiversity conservation were highlighted in the results of this study.