Ancient DNA methodologies can be used to answer questions about extant wild populations such as East African chimpanzees (Pan troglodytes schweinfurthii). In this study, we examine genetic diversity through analysis of both the host genome and the microbial ecosystems within (i.e. the microbiome) using ancient DNA lab methods, shotgun amplification, targeted capture, and Next Generation Sequencing (Illumina). Specifically, the goal of our research at Gombe National Park is to understand the extent to which mitochondrial and oral microbiome diversity has changed over time and how the oral ecosystem from wild chimpanzees compares to that seen in human populations. To date, we have recovered 33 full mitochondrial genomes from chimpanzees living at Gombe between the 1960’s and the 2010’s and found a slight decrease in genetic diversity within the park across decades (0.00257 to 0.00155). Additionally, we report that Gombe chimpanzees showed a significantly higher abundance of the common oral microbial phyla Bacteroidetes and Fusobacteria but a significantly lower abundance of Firmicutes and Proteobacteria when compared to historic human populations. Chimpanzees also showed a higher abundance of the genus Porphyromonas, a microbe associated with the Red Complex, which has been connected to periodontal disease in humans. These results allow us to evaluate the extent to which historic DNA samples (<200 years) can be used to answer questions regarding host health and diversity over time across a variety of at risk wild populations that may benefit from such analyses.