The top-down effects of consumers, such as predators, are known to affect abundances, size structure, and species composition in aquatic ecosystems. Parasites are also important in shaping the ecology of free-living species; however, their effects are often overlooked because parasites can be difficult to detect. Parasites can be particularly challenging to observe in zooplankton hosts because of their small size and ephemeral infection periods. To overcome these challenges, we used a quarantine approach combined with high-magnification microscopy to increase detection of parasites of the tropical Cladoceran, Ceriodaphnia cornuta, in Lake Gatun, Panamá. Using this approach, we were able to demonstrate that competing morphs of Ceriodaphnia experience differential rates of infection, where the subordinate competitor suffered higher parasite prevalence than did the dominant morph. Predation by fishes on the dominant morph is considered the principal mechanism for their coexistence, but we hypothesize that parasites may also play a role in maintaining morphotype diversity of Ceriodaphnia.