This project focused on the identification of bacterial and fungal species in rat feces through 16S and 18S rDNA sequencing. DNA extraction, Polymerase Chain Reaction (PCR), bacterial cloning and sequencing were performed to isolate and identify three bacterial species and one fungal species. Using BLAST sequencing, two bacterial species Neisseria bacilliformis and Neisseria flava were identified successfully. An uncultured bacterial species was also identified; however, the specific species could not be named. The fungal species was identified as Mucor Racemosus, which is commonly found in soil. The processes used in this procedure can be used for further research concerning the microbiome. Identifying bacterial species within the gastro-intestinal tract is important for studying the effects of microbial diversity on human health.