Over recent decades, climate change has led to an increase in the number of species introduced to areas outside their natural ranges. This inevitable increase in the Mediterranean Sea is facilitated through various vectors such as shipping, aquaculture, and escapes/releases from the aquarium trade and most importantly, opening of the Suez Canal. Despite the significant threats posed by non-indigenous species, current research efforts in the Aegean Sea remain fragmented, limiting our understanding of the overall impact of these species and other ecological threats. This study is crucial in providing a comprehensive assessment of the Aegean Sea’s marine ecosystems and offering an up-to-date evaluation of their current state. The non-indigenous species list was compiled based on the existing literature, covering the whole Aegean basin lying between the southern limits being roughly delimited by Kythira, Crete, Karpathos, Rhodes, Datça Peninsula, and the Straits of Çanakkale, and focusing on the vectors of introduction, origins, and observation years of species. A total of 393 non-indigenous species have been listed, with the highest number of species belonging to Mollusca. Since the year 2000, a significant increase in the introduction of non-indigenous species into the Aegean Sea has been observed. By synthesizing scientific literature on the presence of marine non-indigenous species along the Greek and Turkish Aegean coasts, this study establishes a comprehensive baseline for comparative purposes and to contribute to future monitoring efforts.