The purpose of this project was to determine reliable methods for successfully obtaining mitochondrial DNA sequences from an ancient individual. This is made difficult by the DNA's highly degraded nature, as well as its high likelihood for being contaminated. Strict contamination protocols were laid out which each individual working in the lab was required to follow. The methods used were first optimized using a modem DNA sample. These same methods were used on the ancient DNA samples;however more optimization was required to obtain the best results possible from our samples.The GENECLEAN kit for aDNA isolation was used to isolate the DNA from the dentin samples. Approximately 35 µg/mL were obtained from 1.100 g of dentin from the intrusive individual. The next step, PCR, required the most optimization. Multiple runs at varying temperatures and reagents were done to determine which recipe was the most effective for amplifying the isolated DNA. PCR revealed that the isolation was successful and that no contamination had occurred. The TA Topo cloning method required some optimization to determine the best way to grow the colonies and then isolate them for sequencing. The clones were successfully grown. The clones were sent to Davis Sequencing for sequencing and were analyzed using the program Vector NTI. Sequences were obtained from Davis for half of the clones sent. The other half displayed an unexplained primer overlay at one end of the sequence.The samples used in this study were obtained from the Windsor Mound site located in Randolph County, Indiana. The human remains were excavated and curated by the Archaeological Resources Management Service. The Anthropology Department granted permission for the use of the remains for this project, which is in compliance with the Native American Graves Protection and Repatriation Act.