Marine functional connectivity (MFC) refers to the dynamic spatial exchange of biomass, individuals, genes, and energy via the collective movements of all marine organisms during their lifetimes. In addition to controlling the distribution and resilience of marine biodiversity and exploited stocks, MFC plays a key role in the structure and functioning of ecosystems, at sea and at the land-sea interface. As marine ecosystems and their species face climate change and unprecedented multiple anthropogenic pressures, rapid action is needed to comprehend MFC patterns and their changes in order to anticipate the fates of ocean services to humanity. Despite many advances in techniques to measure or infer marine species’ distributions and spatial dynamics, significant progress is still necessary. A full understanding of MFC requires better knowledge of the relationships between marine communities and their habitats, quantification of fluxes of matter and energy, and the capacity to forecast how the many services provided by the ocean may change. The 17 papers in this Theme Section showcase the range of approaches and scales applied in contemporary MFC studies and encompass the diversity of ecosystems and taxa investigated worldwide. The innovative approaches presented here to advance MFC science pave the way to enrich current understanding of MFC’s role in ecosystem functioning, and flag how MFC knowledge can be better applied to protect marine resources and manage marine and littoral habitats.