This publication presents guidelines prepared and adopted by the GFCM to assess and minimize the possible impacts from the use of non-indigenous species in the Mediterranean and the Black Sea. Specifically, it identifies the guiding principles and minimum common criteria needed to minimize the potential adverse impacts of non-indigenous species on biodiversity, natural habitats, ecosystems and related ecosystem services. By recommending practical actions to stakeholders, these guidelines aim to create a common regional framework on aquaculture practices related to the use of non-indigenous species and provide decision-makers with a useful tool for policy development.