The diversity of avian malaria parasites is much greater than 20th century morphologists realized and virtually every study in this field in the last 15 years has uncovered previously undocumented diversity at multiple levels within the taxonomic hierarchy. Despite this explosion of knowledge, there remain vast sampling gaps, both geographically and host-taxonomically, which makes characterizing patterns of diversity extremely challenging. Here, we summarize the current state of knowledge of sub-Saharan African avian malaria parasite diversity, focusing on avian hosts endemic to Africa. The relative proportions of the parasite genera included here, Plasmodium, Haemoproteus (including Parahaemoproteus) and Leucocytozoon, varied between regions, in part due to habitat preferences of the insect vectors of these genera, and in part we believe due to sampling bias. Biogeographic regions of sub-Saharan Africa harbour about the same proportion of endemic to shared parasite lineages, but there appears to be no phylogenetic structuring across regions. Our results highlight the sampling problem that must be addressed if we are to have a detailed understanding of parasite diversity in Africa. Without broad sampling within and across regions and hosts, using both molecular tools and microscopy, conclusions about parasite diversity, host–parasite interactions or even transmission dynamics remain extremely limited.