Heaps of cocoa beans and mucilage placed within plantain leaves in Ekona, Fako Division of the South West Region of Cameroon was studied to isolate and identify bacteria playing a lead role during natural fermentation process. All experiments were performed at JP Johnson Biotechnology Laboratory at IRAD Ekona, Fako Division, South West Region, Cameroon between March – October, 2020. Heaps of 10kg were placed on and covered with plantain leaves and allowed to ferment naturally. Before every sample was collected the temperature and pH were measured. Samples were inoculated into de Mann Rogosa and Sharpe (MRS) agar and Caar agar for the isolation of lactic acid bacteria (LAB) and acetic acid bacteria (AAB) respectively. Standard microbiological procedures for obtaining bacteria counts and isolation of pure cultures were performed and isolated bacteria were identified following morphological and phenotypic characterization on API50CHL for LAB and Enrichment Media for AAB. The fermentation temperature rose to 45oC after 4 days while the pH fluctuated with a peak at 4.82 after 108 hours. Maximum counts of Acetic Acid Bacteria (AAB) (5.8x108 Colony Forming Units (CFU)/ mL) and Lactic Acid Bacteria (LAB) (8.9x8x108 (CFU)/mL were obtained at 2 days and 5 days respectively. Twelve isolates each of AAB and LAB were identified on growth media. After phenotypic characterization, 03 Lactobacillus species and 02 Acetobacter species were identified. The most abundant bacteria were L. plantarum (41.77%) and Acetobacter tropicalis (24.11%) on MRS agar and Caar Agar respectively.L. plantarum and A. tropicalis have been identified as the bacteria playing a lead role in the fermentation of cocoa in Fako Division of the South West Region of Cameroon. These organisms may be used as good candidates in a consortium for use as a starter culture.