Backgroud: Agroforestry systems (SAFs) are an alternative for sustainable development as they enable the recovery of degraded areas and reduce deforestation, contributing to breaking the cycle of traditional family farming, so common in the Amazon region, which enables the recovery of soils , the increase of organic matter and soil fertility. Cocoa beans are grown and fermented in SAFs. According to researches, the significant appearance of endophytic microorganisms such as bacteria in the cocoa bean can benefit its production commonly with fermentative bacteria. The aim of the study was to characterize the microbiota of cocoa beans during the fermentation process. Methods: Bacteria isolation was performed from the collected samples, one of the applied procedures was the scraping of the dried and fermented cocoa beans. Afterwards, aliquots were subcultured in a Petri dish with culture medium containing Blood agar and MacConkey agar to verify bacteria. Cultures were analyzed by counting colony forming units (CFU/mL). Molecular analyses and Sequencing were realized for described the diversity microbial Results: DNA sequencing and phylogenetic analyzes were performed to emphasize microbial morphology characterization. Gram negative bacilli (Enterobacter spp. and Citrobacter spp.) and Gram positive bacilli (Bacillus spp.) were found in cocoa beans after 72 hours of fermentation. Conclusion: However, this work contributed to the characterization of endophytic bacteria in cocoa seeds, enabling in-depth studies of in vitro verification of the potential for biocontrol of these endophytic bacteria in cocoa cultivation.