Marine Protected Areas (MPAs) are vital for biodiversity conservation, yet their effectiveness in preserving foundation seaweeds remains understudied. This study investigates the diversity and distribution of Cystoseira sensu lato (including Cystoseira, Ericaria and Gongolaria) populations in the an MPA located in the central Mediterranean Sea, comparing them with those in two unprotected control sites. We hypothesize that MPA Cystoseira s.l. populations will display higher diversity and structure compared to outside control sites. Results reveal a total of 19 Cystoseira s.l. species at depths of 0-20 m, with the MPA exhibiting a higher diversity than control sites. Thus, MPAs can play a crucial role in fostering the diversity of Cystoseira s.l. populations. However, no significant differences were observed among the MPA's protection zones, raising questions about the zoning effectiveness. Additionally, our survey uncovered a substantial presence of non-indigenous seaweeds within the MPA. In conclusion, while MPAs improve Cystoseira s.l. diversity compared to unprotected sites, the varying efficacy of protection within MPA zones suggests a necessity for site-specific conservation strategies. The presence of non-indigenous seaweeds emphasizes ongoing challenges. This study provides a baseline for understanding Cystoseira s.l. population dynamics, crucial for future monitoring and conservation efforts in the face of climate change.