The objectives of this study were to investigate the change of microorganisms involved in cocoa (Theobroma cacao) fermentation and then to isolate, characterize and select the important microorganisms in cocoa fermentation. The results showed that microbial quantities continuously changed during cocoa fermentation and the highest quantity of dominant microorganisms at different stages of fermentation process as 8.03 log cfu/g of yeast, 6.34 log cfu/g of mold, 7.77 log cfu/g of lactic acid bacteria, 7.87 log cfu/g of acetic acid bacteria, 7.25 log cfu/g of Bacillus, and 10.93 log cfu/g of the total aerobic bacteria. There were nine yeast isolates belonging 5 genera of Saccharomyces, Kluyveromyces, Brettanomyces, Candida and Cystofilobasidium; 9 mould isolates belonging to 2 genera of Rhizopus and Aspergillus; 11 acetic acid bacteria isolates belonging to Acetobacter; and 13 spore-forming bacterial isolates belonging to Bacillus isolates. Three isolates of yeast (CY-1a, CY-1b, CY-2a) belonging to Kluyveromyces possessed the high fermentative capacity and 4 Acetobacter isolates (CAAB-1d, CAAB-1a, CAAB-1e and CAAB-2d) produced high amounts of acetic acid.