Studies on species of Monogenea have shown that these parasites often infect only a specific host species, genus, or family, and that they attach only to specific sites within hosts. Few studies, however, examine habitat specificity across host and habitat scales. In this study, we focused on host, macrohabitat, and microhabitat specificity in the monogenean diplozoon Afrodiplozoon polycotyleus, a gill parasite of African cyprinid fishes, Barbus spp. We first compared the occurrence of A. polycotyleus among 4 species of Barbus from a single location in the Mpanga River of western Uganda; Barbus neumayeri was the only species infected with the parasite. We then quantified parasite prevalence and mean abundance in B. neumayeri from a series of river and swamp sites in the same drainage, looking for environmental predictors of diplozoon prevalence and abundance over a broad habitat scale. The prevalence and mean abundance of A. polycotyleus on gills of B. neumayeri was highest in the hypoxic swamp habitat, followed by the intermittent stream sites, and faster flowing river sites. Parasite prevalence and mean abundance across habitats were negatively related to both water current and dissolved oxygen concentration. Within hosts, A. polycotyleus was strongly specific among hemibranchs in poorly oxygenated water and was found on arch 2, hemibranch 4 most frequently.