Oyster reefs provide critical ecosystem services, including water filtration, shoreline protection, and habitat for marine organisms. However, oyster populations have declined globally, with some species, such as Crassostrea virginica, considered functionally extinct in certain regions. In Biscayne Bay, Florida, C. virginica populations were once abundant historically but have since experienced dramatic declines. Recent findings have identified a remnant C. virginica population spread across various sites in the bay. Oyster aquaculture research at the University of Miami has recently been centered around collecting native C. virginica broodstock in Biscayne Bay to identify areas where this species naturally occurs while simultaneously establishing a broodstock population of native oysters at the University of Miami Experimental Hatchery (UMEH) facility. This work aligns with ongoing efforts to assess the potential of native oysters as a nature-based solution for habitat restoration in Biscayne Bay. In this project, native C. virginica broodstock were collected from sites along the western shoreline of Biscayne Bay, quarantined, transferred to broodstock holding tanks, and finally genotyped using non-lethal sampling methods. Tissue samples were collected after relaxing the oysters in a 5% Epsom salt solution. Given the high variability in shell morphology, molecular analysis was employed for accurate species identification. Genomic DNA was extracted, and mitochondrial cytochrome c oxidase I (COI) gene fragments were amplified using PCR for species identification. DNA sequences were analyzed and compared to reference sequences from other regions. The results confirmed that all oysters sampled (n=43) were C. virginica, with the highest genetic similarity to C. virginica populations from the Gulf of Mexico. The presented results provide a robust protocol for anesthetizing oysters for non-lethal tissue sampling, a molecular approach for assessing oyster species identification in restoration projects, and overall contribute to ongoing efforts to identify and restore oyster habitats in Biscayne Bay, Florida.