Spatially explicit coral bleaching data can be used to improve our understanding of the causes and consequences of coral bleaching and help identify resilient reefs. In 2016, the Great Barrier Reef (GBR) experienced the most severe coral bleaching in recorded history, yet, as in previous 1998 and 2002 events, the severity and spatial extent of coral bleaching were variable. Cyclonic activity mitigated warming effects in the southern GBR, meaning corals in this region were predicted to bleach less; as a result, southern reef areas received little attention. Herein we report the effects of the 2016 warming event on southern inshore reefs around the Keppel Islands, an area of high conservation importance, with a history of environmental disturbance. Surveys of 14 reefs revealed paling of coral colonies at every site. A total of 21% of living coral, primarily Pocillopora and branching Acropora, was affected. Findings suggest that southern reefs were affected by warming, although significantly less than in the north. Records of milder bleaching help delineate variability in bleaching severity and extent across the GBR, and add to the historical record of bleaching history in the Keppel Islands, essential to understanding the complexity of exposure and recovery dynamics of the Keppel reefs.