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Because bioinvasions pose significant threats to marine ecosystems and the goods and services these provide, non-indigenous species (NIS) are included in the more recent legislative documents. A major challenge for the scientific community is to translate the principles of the legislative directives into a realistic, integrated ecosystem-based approach and at the same time provide stakeholders with best practices for managing NIS. The aim of this paper, prepared by members of the Working Group on Introductions and Transfers of Marine Organisms (WGITMO) of the International Council for the Exploration of the Sea (ICES), is to provide guidance for the application of NIS related management in the European Union Marine Strategy Framework Directive (MSFD). Ten recommendations, including NIS identification, standardization of sampling and data, indicators, propagule pressure and management issues are considered in this paper. 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