Compounding pharmacies and contract testing laboratories can readily utilize critical information that microbial identification methods provide. Rapidly identifying the genus and species of environmental isolates and sample contaminates provides pharmacies and laboratories the opportunity to determine the possible source and implement corrective actions to improve compounding and testing processes. The microbial identification data collected from a compounding environment is critical. It is important to have accurate and specific microbial information to guide environmental collection practices, validation studies, and troubleshooting initiatives. The different technologies available provide varying levels of identification. They range from phenotypic assays to more accurate molecular-based techniques, including macromolecular methods and whole genome sequencing. Selecting the appropriate identification methodology requires evaluating multiple factors including the level of information required (genus only, genus and species, etc.) and the pharmacy's tolerance for unidentified or incorrectly identified isolates.