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Abstract Background The current biodiversity crisis underscores the urgent need for sustainable management of the human uses of nature. In the context of sustainability management, adopting the ecosystem service (ES) concept, i.e., the benefits humans obtain from nature, can support decisions aimed at benefiting both nature and people. However, marine ecosystems in particular endure numerous direct drivers of change (i.e., habitat loss and degradation, overexploitation, pollution, climate change, and introduction of non-indigenous species) all of which threaten ecosystem structure, functioning, and the provision of ES. Marine ecosystems have received less attention than terrestrial ecosystems in ES literature, and knowledge on marine ES is hindered by the highly heterogeneous scientific literature with regard to the different types of marine ecosystem, ES, and their correlates. Here, we constructed a systematic map of the existing literature to highlight knowledge clusters and knowledge gaps on how changes in marine ecosystems influence the provision of marine ES. Method We searched for all evidence documenting how changes in structure and functioning of marine ecosystems affect the delivery of ES in academic and grey literature sources. In addition to Scopus, Web of Science, and Google Scholar, we searched 6 online databases from intergovernmental agencies, supranational or national organizations, and NGOs. We screened English-language documents using predefined inclusion criteria on titles, abstracts, and then full texts, without any geographic or temporal limitations. All qualifying literature was coded and metadata were extracted. No formal validity appraisal was undertaken. We identified knowledge clusters and gaps in terms of which ecosystem types, biodiversity components, or ES types have been studied and how these categories are linked. Review findings Our searches identified 41 884 articles published since 1968 of which 12 140 were duplicates; 25 747 articles were excluded at the title-screening stage, then 2774 at the abstract stage. After full-text screening, a total of 653 articles—having met the eligibility criteria—were included in the final database, spanning from 1977 to July 2021. The number of studies was unevenly distributed across geographic boundaries, ecosystem types, ES, and types of pressure. The most studied ecosystems were pelagic ecosystems on continental shelves and intertidal ecosystems, and deep-sea habitats and ice-associated ecosystems were the least studied. Food provision was the major focus of ES articles across all types of marine ecosystem (67%), followed by climate regulation (28%), and recreation (14%). Biophysical values were assessed in 91% of the analysed articles, 30% assessed economic values, but only 3% assessed socio-cultural values. Regarding the type of impact on ecosystems, management effects were the most studied, followed by overexploitation and climate change (with increase in seawater temperature being the most commonly assessed climate change pressure). Lastly, the introduction of non-indigenous species and deoxygenation were the least studied. Conclusions This systematic map provides, in addition to a database, knowledge gaps and clusters on how marine ecosystem changes impact ES provision. The current lack of knowledge is a threat to the sustainability of human actions and knowledge-based nature conservation. The knowledge gaps and clusters highlighted here could guide future research and impact the beneficial development of policy and management practices.