The Ph.D. program in Marine Biology and Ecology (MBE) have the following subject emphases, from which each student chooses a relevant curriculum:

• Coral Reef and Coastal Ecology employs ecological, physiological and molecular approaches to understand, conserve, manage, and restore coral reefs, seagrasses, mangroves and their associated biota.
• Marine Organismal and Biomedical Science focuses on how marine organisms respond to their environment on physiological and evolutionary time scales. This research integrates whole animal and cellular studies of physiology, biochemistry, neurobiology, genomics, molecular biology, aging, pathology and toxicology to understand factors controlling these responses and to develop these systems as models for human health.
• Biological Oceanography focuses on adaptations, ecological interactions, food webs, and biogeochemical cycles of the ocean.
• Fisheries Science studies the direct and indirect impacts of living marine resource exploitation on marine populations, communities and habitats and investigates solutions to the problems of unsustainable, habitat-damaging and/or inefficient fishing, including the minimization of bycatch and food web disruption.