Metagenomics is an emerging field in which the power of genomic analysis (analysis of DNA in an organism) is applied to entire communities of microbes bypassing the need to isolate and culture individual microbial species. Our goal was to determine the prevalence and persistence of endophytic microbes in muscadine grape. Muscadine grape (cv. Noble) berries were collected from the core germplasm repository of the FAMU Center for Viticulture, Tallahassee and analyzed. The samples were serially diluted in saline and inoculated onto YM and PDA media for fungus and LB, and nutrient agar for bacteria. Total DNA was isolated from both skin and pulp (with seed) tissue using Zymo Research kit according to manufacturer’s instructios from both fungal and bacterial cultures. PCR was performed using 16S bacterial and 26S fungal rRNA primers. The PCR products obtained were cloned and sequenced to identify microbial community present in muscadine berries. The sequence data from pulp (with seed) tissue (cv. Noble) revealed presence of one bacterial species, Gluconacetobacter sacchari and 57 fungal species. The recovered fungal clones were sorted into six taxonomical units, and majority of the clone sequences were assigned to Ascomycota, while only one bacterial clone could be identified as Proteobacterium. On berry skin tissue, one fungal species, Cladosporium was predominant. Among the identified fungal species few were annotated to endophytic species that are known to produce novel compounds beneficial to both plants and humans. Further analysis is being carried out to determine proteins and metabolites generated by these microbial communities.