Recently, an underwater version of a fast repetition rate fluorometer (FRRF) was developed for the non-destructive study of fluorescence yields in benthic photoautotrophs. We used an FRRF to study bleached colonies of the corals, Montastraea faveolata and Diploria labyrinthiformes at sites surrounding Lee Stocking Island, Exuma, Bahamas, to assess their recovery from bleaching (∼1 year after the initial bleaching event) induced by elevated temperatures. The steady state quantum yields of chlorophyll a fluorescence (ΔF′/F′m) from photosystem II (PSII) within coral colonies were separated into three categories representing visibly distinct degrees of bleaching ranging from no bleaching to completely bleached areas. Differences in ΔF′/F′m were significantly different from bleached to unbleached regions within colonies. Dark, unbleached regions within colonies exhibited significantly higher ΔF′/F′m values (0.438±0.019; mean±S.D.) when compared to lighter regions, and occupied a majority of the colonies’ surface area (46–73%). Bleached regions exhibited significantly lower ΔF′/F′m (0.337±0.014) and covered only 7–25% of the colonies’ surface area. The observations from this study suggest that zooxanthellae in bleached regions of a colony exhibit reduced photosynthetic activity as long as one year after a bleaching event and that in situ fluorescence techniques such as FRRF are an effective means of studying coral responses and recovery from natural or anthropogenic stress in a non-destructive manner.