To understand the ancestral microorganisms within the human oral cavity, it is imperative to examine the oral ecosystem of closely related primate species. Dental calculus (calcified plaque) allows for the investigation of long-term microbial genetic information, but has yet to be fully explored within non-human primates. We present results from shotgun prepared, Illumina sequenced dental calculus DNA libraries in order to understand the microbial diversity of wild chimpanzees compared to humans. We compare dental calculus from 16 deceased chimpanzees belonging to the Kasekela community spanning 50 years of occupation at Gombe National Park. These samples are dominated by the microbial phyla Spirochaetes, TM7, and Euryarchaeota, and significantly differ from phyla commonly found within human plaque. We also investigate the presence of ‘Red Complex’ bacteria within chimpanzees, a group of microbes thought to be associated with periodontal disease in human populations. We discuss how these results fit into our current knowledge of primate oral ecosystems and the implications of these findings for human health and evolution.