We examine the relationship between geographic location and population sub-structure among chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) across Africa using a set of new and previously published mitochondrial DNA data. We analyzed 1011 HVR1 and 45 mitochondrial genome (mtgenome) geo-referenced sequences. Included in these data are nine new mtgenome sequences obtained from DNA extracted from the dentin and dental calculus of chimpanzees buried at Gombe National Park. Genetic analyses of the Gombe chimpanzees did not begin until the early 1990s, and our analyses show poor DNA preservation in dentin from individuals buried there prior to that time. However, mtgenome sequences were recoverable from dental calculus. Median network analyses identify distinguishable local clusters of mtDNA lineages within all chimpanzee subspecies as well as bonobos. Mismatch distribution analyses and estimates of Tajima’s D and Fu’s F indicate historical population expansion in P.t.schweinfurthii but not in the other groups, corroborating previously published research. Our preliminary insights are being expanded by Spatial Principal Components analyses and Bayesian inference on both the HVR1 and complete mtDNA datasets. Samples of unconfirmed geographic origin are being added to these analyses to determine if the structures observed remain unchanged. If successful, this research may allow the estimation of the geographic area of origin of individuals with unknown histories beyond a simple sub-species classification. This is the first attempt at a genus-wide spatial analysis with a large sample size across all members of the genus Pan.