Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07% of the taxa detected by a broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean. Coastal regions make up less than 10% of the Earth's surface but their ecosystems contribute disproportionately to the globe's primary productivity, biodiversity, and ecosystem services 1-4. Coral reefs alone are thought to be home to 25% or more of described marine species 5. Human activities such as coastal development, exploitative fishing practices, and eutrophication, however, have resulted in the widespread decline of commercially-important fisheries, the loss of important habitat-forming species, and biological invasions 6-8. The accelerating pace of changes in the structure and function of coastal ecosystems due to these impacts makes it urgently important to develop methods for efficient and effective biomonitoring to support management, conservation, and basic science initiatives 9. Systematic survey data are especially fundamental in understanding the link between biodiversity and the health and functioning of marine ecosystems 10-12. At its core, biomonitoring requires the reliable identification of species that are present in an environment, and answers if, how, and why populations of these species change over time. Yet, it still remains a challenge to capture the full taxonomic diversity of ecosystems in a repeatable way to identify trends through time and patterns across space 13. Traditional marine biodiversity surveying methods, such as visual surveys by divers, are often expensive, invasive, require taxonomic expertise, are limited by visibility or habitat complexity, and miss cryptic diversity, including most invertebrates 14-16. As a result, such traditional
