Coral reefs represent one of the most diverse ecosystems globally but today are experiencing some of the greatest anthropogenic impacts. Overfishing, pollution and climate change are the three biggest threats to coral reefs, and is reflected by increasing coral mortaility and proliferating macro-algae and bactierial species. We question whether this transition from healthy to dead coral habitat increases the susceptibility of resident fishes to disease. Fish gills exhibit unique bacterial communities that can act as a first line defence against diseases and pathogens, but it is unknown how this important community may be affected by habitat-borne pathogens. We investigated how the gill microbial communities of five tropical coral reef fishes responded to three habitat scenarios: a) healthy live coral (Pocillopora damicornis), b) dead algae-covered coral, and c) ambient seawater, to mimic pelagic conditions (control). Linking habitat degradation with the types and levels of pathogens found on the gills of several species of coral reef fishes will help define the health and state of resident fishes. Utimately this information can provide more effective fisheries management and conservation of coral reef fishes by providing further protection to commercially important species (e.g. coral trout) and urge policy makers to mitigate anthropogenic threats.