Different protozoa and metazoa have been detected in great apes, monkeys and humans with possible interspecies exchanges. Some are either nonpathogenic or their detrimental effects on the host are not yet known. Others lead to serious diseases that can even be fatal. Their survey remains of great importance for public health and animal conservation. Fecal samples from gorillas (Gorilla gorilla) and humans living in same area in the Republic of Congo, chimpanzees (Pan troglodytes) from Senegal and one other from the Republic of Congo, Guinea baboons (Papio papio)from Senegal, hamadryas baboons (Papio hamadryas) from Djibouti and Barbary macaques(Macaca sylvanus) from Algeria, were collected. DNA was extracted and screened using specific qPCR assays for the presence of a large number of helminths and protozoa. Positive samples were then amplified in standard PCRs and sequenced when possible. Overall, infection rate was 36.5% in all non-human primates (NHPs) and 31.6% in humans. Great apes were more often infected (63.6%) than monkeys (7.3%). At least twelve parasite species, including ten nematodes and two protozoa were discovered in NHPs and five species, including four nematodes and a protozoan in humans. The prevalences ofGiarida lamblia,Necator americanus, Enterobius vermicularis, Strongyloides stercoraliswere similar between gorillas and human community co-habiting the same forest ecosystem in the Republic of Congo. In addition, human specificMansonella perstans(5.1%) and otherMansonellaspp. (5.1%) detected in these gorillas suggest a possible cross-species exchange. Low prevalence (2%) ofAscaris lumbricoides, Enterobius vermicularis, Strongyloides stercoraliswere observed in chimpanzees, as well as a high prevalence ofAbbreviata caucasica(57.1%), which should be considered carefully as this parasite can affect other NHPs, animals and humans. The Barbary macaques were less infected (7.2%) andOesophagostomum muntiacumwas the main parasite detected (5.8%). Finally, we report the presence ofPeloderasp. and an environmental Nematoda DNAs in chimpanzee feces,Nematodasp. andBodosp. in gorillas, as well as DNA of uncharacterized Nematoda in apes and humans, but with a relatively lower prevalence in humans. Prevalence of extraintestinal parasites remains underestimated since feces are not the suitable sampling methods. Using non-invasive sampling (feces) we provide important information on helminths and protozoa that can infect African NHPs and human communities living around them. Public health and animal conservation authorities need to be aware of these infections, as parasites detected in African NHPs could affect both human and other animals' health.