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Climate change, mismanaged resource extraction, and pollution are reshaping global marine ecosystems with direct consequences on human societies. Sustainable ocean development requires knowledge and data across disciplines, scales and knowledge types. Although several disciplines are generating large amounts of data on marine socio-ecological systems, such information is often underutilized due to fragmentation across institutions or stakeholders, limited standardization across scale, time or disciplines, and the fact that information is often not searchable within existing databases. Compiling metadata, the information which describes existing sets of data, is an effective tool that can address these challenges, particularly when metadata corresponding to multiple datasets can be combined to integrate, organize and classify multidisciplinary data. Here, using Mexico as a case study, we describe the compilation and analysis of a metadatabase of ocean knowledge that aims to improve access to information, facilitate multidisciplinary data sharing and integration, and foster collaboration among stakeholders. We also evaluate the knowledge trends and gaps for informing ocean management. Analysis of the metadatabase highlights that past and current research in Mexico focuses strongly on ecology and fisheries, with biological data more consistent over time and space compared to data on human dimensions. Regional imbalances in available information were also evident, with most available information corresponding to the Gulf of California, Campeche Bank and Caribbean and less available for the central and south Pacific and the western Gulf of Mexico. Despite existing knowledge gaps in Mexico and elsewhere, we argue that systematic efforts such as this can often reveal an abundance of information for decision-makers to develop policies that meet key commitments on ocean sustainability. Surmounting current cross-scale social and ecological challenges for sustainability requires transdisciplinary approaches. Metadatabases are critical tools to make efficient use of existing data, highlight and address strengths and deficiencies, and develop scenarios to inform policies for managing complex marine social-ecological systems.