The Mediterranean Sea, a biodiversity hotspot, faces significant threats from non-indigenous species (NIS), which drive biodiversity changes. Over the past century, the introduction of NIS has accelerated due to maritime traffic, aquaculture, and interoceanic canals, fostering biological invasions. Marine protected areas (MPAs), established to preserve biodiversity, are increasingly impacted. This review quantified and characterized French Mediterranean MPAs, analyzing non-indigenous macroalgae distribution based on the existing literature and the authors' observations. Results revealed widespread occurrence, with the highest NIS richness in strictly regulated MPAs; their proximity to large harbors highlights the paramount importance of the introduction pathways. In addition, there is a significant knowledge gap regarding the distribution of NIS within MPAs, complicating efforts to monitor and study these species effectively. These findings highlight the challenges in monitoring and managing invasions and the urgent need for controlling primary and secondary invasion pathways, within and outside the MPAs, international collaboration to control them, and enhanced funding for NIS monitoring. Without adaptive management, even strictly protected MPAs are vulnerable to the escalating impacts of invasive species.