The first stage in chocolate production is a microbial fermentation of cocoa beans. Several groups of microorganisms are responsible of numerous biochemical and physical changes inside and outside the beans. Classical microbiological methods fail to detect most microbial species. Therefore, molecular methods, such as Polymerase Chain Reaction - Denaturing Gradient Gel Electrophoresis (PCR-DGGE) fingerprinting was utilized to assess the microbial ecology of cocoa fermentation. In this study the microbial ecology of wood box fermentation from Ivory Coast was investigated using 16S rDNA and 26S rDNA to detect variations in the ecology structure of bacteria and yeasts, and populations of individual species were determined at three time intervals by sequencing of DNA purified from DGGE gels. Analyses of DGGE patterns show that cocoa beans fermentation generated great variations in the microbial ecology in terms of number of species and their relative abundance. The bacterial ecology quickly undergoes dramatical changes during the process after two days of fermentation the dominance of Enterobacteria, first with Lactic acid bacteria and at the lastest stages by acetic acid bacteria. Furthermore, the yeast Hanseniaspora opuntiae predominated during cocoa bean fermentation as its abundance remain stable throughout the whole process. Other yeast species showed great variations in abundance along the process (arise or disappear).