Coral reefs, the most biodiverse of all marine ecosystems, are of high ecological, cultural, and financial importance, yet they are declining on a global scale due to several anthropogenic factors. Current threats to coral reefs highlight the urgent need for effective research, monitoring, and management of these ecosystems. In this case study-based exercise, students will compare and contrast biodiversity information about Hawaiian reefs between traditional diver surveys and eDNA based applications, consider the benefits and limitations of each method for coral reef fish monitoring, and use these data to designate potential marine protected areas (MPAs). As part of this process, they will practice identifying species based on genetic sequencing data using the Basic Local Alignment Search Tool (BLAST) of the National Center for Biotechnology Information. Lastly, students will be introduced to different approaches to protection of marine systems in Hawai‘i, including the Papahānaumokuākea Marine National Monument, and reflect on the diversity of approaches to management of seascapes.