A comparative vulnerability analysis of 16 selected benthic habitat types in the SE Baltic Sea waters and the Curonian lagoon, including Klaipeda strait, was performed using long-term monitoring datasets (1980-2003) and results of several other surveys in the lagoon and the sea. Results indicated that invasive species richness (number of alien species per habitat) in lagoon habitats was significantly higher than in the sea. Habitats formed by artificial rock and stone, sand, mud, and habitats modified by zebra mussel shell deposits appeared to be the most invaded. Highest invasive species richness occurred in habitats with high native species richness indicating that the main factors driving native species distribution (such as favourable physical conditions, habitat alterations generated by human or/and biotic activities) are also driving aquatic invaders. Physical factors distinguished to be the most important for native and invasive species distribution were salinity, depth range (expressed by the maximal and minimal depths difference within a habitat), shallowness of a habitat (expressed by a minimal depth), and availability of a hard substrate.