The field of Wildlife Forensics currently lacks a method for genetically discriminating between Bald and Golden Eagles from low-quality DNA samples. Such a method would be useful for investigating cases where only small or contaminated samples of DNA are available. Currently, a genetic marker in the cytochrome b region of mitochondrial DNA (mtDNA) can be used with high quality samples to discriminate between the species. The goal of this research is to develop a mtDNA marker that can be used on small and contaminated samples with good accuracy. DNA was extracted from eagle blood and tissue samples. The polymerase chain reaction (PCR) was used to amplify this region of mitochondrial cytochrome b. Amplified fragments were sequenced and aligned with known eagle sequences. New primer sets were designed for mtDNA to amplify this region with greater yield for both species. This technique will be refined to discriminate between the species.