This study addresses the coupled themes of science and conservation by characterizing and evaluating the coral reefs around Yap, Federated States of Micronesia. Reef types, and the inherent environmental regimes they constitute, were found to be good predictors of distinct modern assemblages, with minimally overlapping species occurrences. Corals from inner and channel reefs were twice as large and assemblages were half as diverse compared with outer reefs, while food-fish were both larger and more diverse on outer and channel reefs compared with inner. While distinctions were predictable, the magnitude of ecological change along a gradient of inner, channel, to outer reefs was higher than expected, suggesting that human influences are quantifiable. Therefore, an evaluation process was conducted to determine the spatial trends in reef ‘condition’, defined within by ecological metrics. ‘Condition’ was highest for reefs associated with a priori defined high conservation value for varying reasons: successful fisheries management, critical habitat determination, and high resiliency potential. Regression analyses highlighted that a two-variable model which interactively incorporated proxies to fishing and pollution, as well as a proxy for hydrodynamic flushing potential, explained 40 % of the variance in ‘condition’. Collectively, the results are used to evaluate the current status of reef assemblages, and to point out future conservation priorities.