Parasites are ubiquitous in nature but assessing their prevalence in wild fish populations is often challenging due to their cryptic nature. Low abundance can also hinder detailed studies. Here, we report a relatively high prevalence (4.3%; range = 0–28%) of an ectoparasitic cymothoid isopod (Anilocra nemipteri) infecting the bridled monocle bream (Scolopsis bilineatus) on reefs surrounding Lizard Island on the northern Great Barrier Reef (GBR). The prevalence of infected and previously infected fish at this location was nearly 15%, which greatly exceeds reports from other localities on the GBR. At least one parasitised fish was observed at 75% of the reefs surveyed, although prevalence varied across sites. Parasitised S. bilineatus were, on average, 25% smaller than unparasitised or previously parasitised fish. Given that these parasites have known detrimental effects on host growth, survivorship and swimming ability, our observations suggest that A. nemipteri may influence the size structure of its host population in the wild. Since A. nemipteri is large, conspicuous and relatively abundant, it provides an ideal study system to examine a range of important questions on the evolutionary ecology of parasites.