The tropical environment of Gombe National Park, Tanzania makes the recovery of endogenous genetic material from skeletal remains inherently difficult. Since the 1960’s many of the Pan troglodytes schweinfurthii skeletons were interred under circumstances not conducive to adequate DNA preservation. To date, no skeletal material has yielded usable DNA, despite the relatively young age of the samples. Here, for the first time, using novel extraction methods, we capture chimpanzee DNA from dentin and calcified dental plaque (calculus) in order to address questions about overall preservation and genetic diversity within several generations of Gombe National Park inhabitants. DNA was extracted from a total of 28 chimpanzees (9 dentin and 28 calculus samples) and built into double-stranded shotgun libraries. Amplified libraries underwent in-solution hybridization capture enrichment and were sequenced on an Illumina MiSeq (v2, 2x150 paired end) in order to obtain complete mitochondrial genomes (mitogenomes). We were able to reconstruct successfully the mitogenomes from all 9 dentin samples (240x mean coverage at 100%) and 28 calculus samples (37x mean coverage at 98%). We used mitogenomes to conduct an exploratory survey of genetic diversity over time at Gombe. When combined with publicly available P.t. schweinfurthii HV1 data, we found that haplotype diversity of chimpanzees who died before 1992 was slightly higher than those who died after (0.862 compared to 0.824). These preliminary results mark the first mitogenomes reconstructed from deceased Gombe chimpanzee calculus and further validate the use of the biological material as a reservoir for host DNA.