Gnathiid isopods, common fish ectoparasites, can affect fish physiology, behaviour and survival. Gnathiid juveniles emerge from the benthos to feed on fish blood. In the Caribbean, gnathiids are positively associated with dead coral and negatively associated with live coral, due to coral predation on gnathiids. However, such interactions were unstudied in the Great Barrier Reef (GBR). Due to recent extreme weather events (two cyclones and one mass warm-water coral bleaching event, 2014-2016), it is now urgent to understand the role of corals on the abundance of these ectoparasites. Here, to understand parasite-coral dynamics at the micro-habitat level, we examined substrate associations of gnathiid isopods on Lizard Island (GBR) using demersal plankton emergence traps. Additionally, we determined whether two abundant hard coral species, Goniopora lobata and Pocillopora damicornis, predate on gnathiids in a laboratory experiment using containers with gnathiids and fragments from each coral species or dead coral as controls. The abundance of gnathiids over natural substrates was higher for dead compared to live hard coral and sand, but not live soft coral. Moreover, we found that free-swimming gnathiids decreased in containers with live coral compared to dead coral controls. This was attributed to predation as we also directly observed a coral ingesting a gnathiid. Our results suggest that dead coral is a suitable microhabitat for gnathiids, but that live coral is not since live corals can predate on gnathiids. We propose that following extreme events, such as cyclones and heat waves, gnathiids might benefit from more dead coral substrate and a decrease in predation by the reduction in coral cover on the reef. We advocate that an increase in the frequency of extreme events may have cascading effects for the fish population through changes in the population of benthos-dependent ectoparasites.