We examined the microbial ecology of shallow reefs within the Federated States of Micronesia. We surveyed 20 reefs surrounding seven islands and atolls (Yap, Woleai, Olimarao, Kosrae, Kapingamarangi, Nukuoro and Pohnpei), spanning 875,053 km2. Divers documented benthic life and fishes. Surface and reef-depth seawater were sampled to examine nutrients, phytoplankton composition, and microbial abundances and community composition (using SSU rRNA gene characterizations).