Non-indigenous species (NIS) are recognized as a global threat to biodiversity and monitoring their presence and impacts is considered a prerequisite for marine environmental management and sustainable development. However, monitoring for NIS seldom takes place except for a few baseline surveys. With the goal of serving the requirements of the EU Marine Strategy Framework Directive and the EU Regulation on the prevention and management of the introduction and spread of invasive alien species, the paper highlights the importance of early detection of NIS in dispersal hubs for a rapid management response, and of long-term monitoring for tracking the effects of NIS within recipient ecosystems, including coastal systems especially vulnerable to introductions. The conceptual framework also demonstrates the need for port monitoring, which should serve the above mentioned requirements but also provide the required information for implementation of the International Convention for the Control and Management of Ships Ballast Water and Sediments. Large scale monitoring of native, cryptogenic and NIS in natural and man-made habitats will collectively lead to meeting international requirements. Cost-efficient rapid assessments of target species may provide timely information for managers and policy-advisers focusing on particular NIS at particular localities, but this cannot replace long-term monitoring. To support legislative requirements, collected data should be verified and stored in a publicly accessible and routinely updated database/information system. Public involvement should be encouraged as part of monitoring programs where feasible. •Monitoring of non-indigenous and cryptogenic species/populations needs to be initiated.•Monitoring should focus on bridgehead sites and dispersal hubs.•Monitoring methods should be internationally harmonized.•Rapid assessments of particular species may provide timely but limited information.•Monitoring data should be assembled in open access continually updated databases.