Abstract - Vietnam's oldest marine protected area, the Con Dao Archipelago, hosts a high diversity of fishes, but they are not taken into account in its management. Knowledge of the spatial and temporal diversity of fishes is critical to identify the ecological functions of protected habitats, including as nurseries and feeding grounds. One way to assess diversity is using light traps that target young fish stages. Fish were collected monthly from June 2016 to May 2017 using light traps in three main habitats: seagrass beds, coral reefs and the harbour. Morphometry and DNA barcoding were used to identify the species caught. A total of 11,293 fish were collected, of which 1,248 were barcoded and assigned to 158 species belonging to 81 genera and 34 families, evidence that coral reefs and seagrass beds in Con Dao marine protected area (MPA) are home to a highly diverse and abundant community of fish species. Species richness and Shannon diversity indices did not differ significantly among sampling sites, but both species composition and diversity indices differed in the wet and dry seasons. The abundance of fish was related to sea water temperatures, which varied significantly depending on the month. During the dry season, fish diversity peaked in April, when the water temperature was highest. Conserving fish in Con Dao MPA is important not only for the characterization of the trophic network in coral reefs and seagrass beds but also for preservation of coral reef ecosystems and endangered species. Ensuring connectivity between coral reefs and seagrass beds in Con Dao MPA would facilitate fish conservation but, at present, the MPA only focuses on protecting fragmented habitats that are home to a number of endangered mammal species. Local authorities should establish a continuum of protected areas along coastal habitats and seasonal controls on fishing as part of sustainable management of MPAs.