This study presents the first comprehensive assessment of alien species occurrences within the selected 11 Marine Protected Areas (MPAs) located on the Aegean and Levantine coasts of Turkey. The inventory includes a total of 289 species belonging to 15 phyla, in which lowest and highest diversities were observed in Saros Bay MPA (27 species, northern Aegean Sea) and Fethiye-Göcek Bay MPA (150 species, northwest Levantine Sea), respectively. Alien species distributions that were revealed in protected areas located in the southern Aegean and Levantine Seas were 56.9% similar (based on presence vs. absence data), while northern Aegean sites formed another distinct group. According to the breakdown of major phyla through the entire study areas, Mollusca had the highest alien diversity (22.1% of alien species), followed by Actinopterygii (19.0%), Arthropoda (15.2%) and Annelida (13.5%). Casual aliens were represented by very low proportions in each MPA, proving that most species were already established in the region, with a significant proportion of invasive species. Regardless of the localities, the majority of the species originated from the Red Sea, whose primary pathway of introduction is the corridor, the Suez Canal. In the absence of effective management actions against bioinvasions, MPAs located along the Turkish coastline do not currently seem to provide any protection, revealing a large conservation gap to be filled.