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Mass coral bleaching events due to rising seawater temperatures are occurring with increasing frequency and are among the most conspicuous consequences of human-induced climate change. While bleaching events have clear impacts on the corals themselves, the impacts on other organisms and on the overall reef community are more difficult to assess. This is particularly true for parasitic organisms, which in spite of their high diversity and biomass are typically ignored in ecological monitoring studies. Here, we take advantage of long-term monitoring of host-parasite-cleaner interactions on experimental patch reefs to assess the effects of mass bleaching events on gnathiid isopod populations around Lizard Island, Great Barrier Reef. Compared with non-bleaching years, gnathiid abundance was consistently low during the warm-water period in bleaching years, but rebounded during the cooler months. This pattern is likely due to the interaction between the short-term negative impacts of thermal stress and declines in hosts on gnathiids, combined with the longer-term positive impacts of declines in cleaner wrasses and of increased dead coral on gnathiid abundance.