The main objective of recent international legislative measures and policies concerning marine ecosystems is to ensure sustainable environmental management to maintain a good status for marine waters, habitats and resources, with the ultimate target of achieving an integrated ecosystem-based approach to management. 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. While most of these suggestions were developed to improve the implementation of the MSFD, several may be more widely applicable. © 2013 Elsevier Ltd.