Connectivity is a crucial process underpinning the persistence, recovery, and productivity of marine ecosystems. The Convention on Biological Diversity, through the Aichi Target 11, has set the ambitious objective of implementing a ‘well connected system of protected areas’ by 2020. This paper identifies eight challenges toward the integration of connectivity into MPA network management and planning. A summary table lists the main recommendations in terms of method, tool, advice, or action to address each of these challenges. Authors belong to a science–management continuum including researchers, international NGO officers, and national MPA agency members. Three knowledge challenges are addressed: selecting and integrating connectivity measurement metrics; assessing the accuracy and uncertainty of connectivity measurements; and communicating and visualizing connectivity measurements. Three management challenges are described: integrating connectivity into the planning and management of MPA networks; setting quantitative connectivity targets; and implementing connectivity-based management across scales and marine jurisdictions. Finally, two paths toward a better integration of connectivity science with MPA management are proposed: setting management-driven priorities for connectivity research, bridging connectivity science, and MPA network management. There is no single method to integrate connectivity into marine spatial planning. Rather, an array of methods can be assembled according to the MPA network objectives, budget, available skills, data, and timeframe. Overall, setting up ‘boundary organizations’ should be promoted to organize complex cross-disciplinary, cross-sectoral and cross-jurisdiction interactions that are needed between scientists, managers, stakeholders and decision-makers to make informed decision regarding connectivity-based MPA planning and management.