The microbiome of non-human primates is relatively neglected compared with humans, and yet it is a source of many zoonotic diseases. We used high throughput sequencing of circulating cell-free DNA to identify the bacteria, archaea, eukaryotic parasites and viruses from over 200 individual non-human primates across 17 species from Africa. Many of the assembled sequences have low or no homology to previously sequenced microorganisms, while those that do have homology support prior observations of specific taxa present in primate microbiomes. The structure of the total microbiome is correlated with geographic location, even between distinct primate species which are co-located. However, we find that viruses have a particularly notable association with host taxa independent of geography. Numerous potentially zoonotic taxa were discovered in an unbiased manner, thereby expanding knowledge of host species diversity and strengthening the case for monitoring wildlife reservoirs.One Sentence Summary: Blood from non-human primates provides insight into potential pathogens which might eventually infect humans.