Non-indigenous species (NIS) represent a water quality descriptor in the Marine Strategy Framework Directive (MSFD) because they pose a major threat to biodiversity. The Azores have 26 species of marine macroalgae identified as NIS, twice the world trend. With 6 coherently articulated tasks, the CRYPTO Project aims to detect NIS among the 40 cryptogenic species in the Azores and assess the respective invasive risks.