Coral bleaching, triggered by elevated sea-surface temperatures (SSTs) has caused a decline in coral cover and changes in the abundances of corals on reefs worldwide. Coral decline can be exacerbated by the effects of local stressors like turbidity, yet some reefs with a natural history of turbidity can support healthy and resilient coral communities. However, little is known about responses of coral communities to bleaching events on anthropogenically turbid reefs as a result of recent (post World War II) terrestrial runoff. Analysis of region-scale coral cover and species abundance at 17-20 sites on the turbid reefs of Okinawa Island (total of 79 species, 30 genera, and 13 families) from 1995 to 2009 indicates that coral cover decreased drastically, from 24.4% to 7.5% (1.1%/year), subsequent to bleaching events in 1998 and 2001. This dramatic decrease in coral cover corresponded to the demise of Acropora species (e.g., A. digitifera) by 2009, when Acropora had mostly disappeared from turbid reefs on Okinawa Island. In contrast, Merulinidae species (e.g., Dipsastraea pallida/speciosa/favus) and Porites species (e.g., P. lutea/australiensis), which are characterized by tolerance to thermal stress, survived on turbid reefs of Okinawa Island throughout the period. Our results suggest that high turbidity, influenced by recent terrestrial runoff, could have caused a reduction in resilience of Acropora species to severe thermal stress events, because the corals could not have adapted to a relatively recent decline in water quality. The coral reef ecosystems of Okinawa Island will be severely impoverished if Acropora species fail to recover.