Abstract Biological health underpins ecosystem services, including the production of food from the sea. Therefore, many policy frameworks rely on biological observations to guide the sustainable use of marine resources. For example, a marine biodiversity observation network can provide evidence of ecosystem degradation, remediation success, and progress toward goals of sustainable development. The utility of biodiversity observations is limited, however, if measurements are not standardized to allow comparisons across space and time or if they are too difficult or expensive to make routinely or at large scale. Molecular approaches (e.g., metagenomics, metabarcoding, eDNA, metatranscriptomics) offer efficiencies in sample collection and processing and provide analysis across trophic levels compared to traditional methods. Increased affordability and throughput of nucleic acid sequencing allow integration of molecular biological techniques into operational monitoring with the potential benefit of expanding the spatial and temporal scale of biological observations.