Bacteria play an important role in the fermentation process of the cocoa bean. For example, bacteria from the genus Acetobacter oxidize ethanol, produced by yeast, to form acetic acid. While the acetic acid is formed during the cocoa fermentation, the temperature increases due to biochemical reactions, killing germs and breaking the cell wall. Therefore, these compounds within cells had the opportunity to interact with each other to form new chemical compounds. The presence of numerous chemical compounds during fermentation enhances the color and quality of cocoa beans. Fermentation is the most important step in cocoa processing as it contributes to the flavor, color and texture characteristics of cocoa beans used in making chocolate. Morphological characterizing methods and sequence analysis of 16S rRNA genes were used in this study for identifying some bacterial species. The results show that the number of CFU ranged from 1.8 x 10 4 to 7.2 x 10 7 CFU/g of fresh cocoa beans. In total, 11 different colony morphologies belonging to 7 species of bacteria were isolated and identified, showing 99-100% similarity to Genbank sequences. The species include Acetobacter tropicalis, Acetobacter pasteurianus, Acetobacter indonesiensis, Acinetobacter calcoaceticus, Microbacterium oxydans, Sphingomonas melonis, and Serratia marcescens.