The relevance of spatial variation in the environment and host communities for parasite community composition is poorly documented, creating a need for additional case studies from which general principles can be developed. Avian malaria in southern African waterfowl has not previously been studied. As a first step towards documenting and understanding its biogeography, we used PCR and molecular sequencing techniques to analyse 454 blood samples from Afrotropical ducks from 5 different locations (spread around the subregion) for avian malaria. Fifty-five blood samples were positive for one or more genera of haematozoa. The regional infection rate across all sites and sampling periods was 12·1%. Nine individuals carried dual infections containing multiple haematozoa. Fifteen different cytochrome b haplotypes among 52 positives (3 samples failed to sequence) and 61 total sequences were found. Eleven haplotypes closely matched Plasmodium, whereas 4 were more similar to Haemoproteus. Five distinct haematozoan clades were identified. Haemoproteus parasites appeared to be more host-specific than Plasmodium, which occurred at every sampling location and in every host species examined. There were no significant differences in overall parasite prevalence attributable to either site or species, although Plasmodium and Haemoproteus occurrences differed by site-species combination and the borderline significance of our test for between-site variation (P < 0·06) implied that with a larger sample size, differences in parasite prevalence among locations might be detectable.