The oncogenic Merkel cell polyomavirus (MCPyV) infects humans worldwide, but little is known about the occurrence of viruses related to MCPyV in the closest phylogenetic relatives of humans, great apes. We analyzed samples from 30 wild chimpanzees and one captive gorilla and identified two new groups of polyomaviruses (PyVs). These new viruses are by far the closest relatives to MCPyV described to date, providing the first evidence of the natural occurrence of PyVs related to MCPyV in wild great apes. Similar to MCPyV, the prevalence of these viruses is relatively high (>30%). This, together with the fact that humans in West and Central Africa frequently hunt and butcher primates, may point toward further MCPyV-like strains spreading to, or already existing in, our species.