Mantchoua is a fermented seed condiment produced from kapok tree (Ceiba pentandra) seeds in Burkina Faso. In this study, the microbiology of Mantchoua from raw material to final product was investigated in samples from two production sites (Po and Bobo-Dioulasso). Four processing methods of Mantchoua production were characterized by determination of numbers of Aerobic Mesophilic Bacteria (AMB), Bacillus spp. and pH. A total of 251 Bacillus spp. from 619 AMB isolates were identified using M13-PCR and ITS-PCR typing, 16S rRNA and gyrA gene sequencing. AMB and Bacillus spp. counts in raw material ranged between 4.2-4.7 log10 CFU/g and 3.8-4.1 log10 CFU/g in kapok seeds and between 2.2-2.3 log10 CFU/g and 1.1-1.8 log10 CFU/g in ash lye solution, respectively. Microbial counts in seeds mash during fermentation ranged between 9-10.9 log10 CFU/g for AMB and between 8.6-10.5 log10 CFU/g for Bacillus spp. In dried Mantchoua, AMB counts ranged between 7.7-10.4 log10 CFU/g while Bacillus spp. counts ranged between 7.5-10.3 log10 CFU/g. The fermentation of Mantchoua involved different species of Bacillus spp. At Bobo-Dioulasso pilot plant, B. subtilis subsp. subtilis dominated (50% of the Bacillus isolates) followed by B. cereus sensu lato (28% of the Bacillus isolates) while at Po traditional production site, B. cereus sensu lato dominated (54% of the Bacillus isolates) followed also by B. subtilis subsp. subtilis (26% of the Bacillus isolates). For the Mantchoua processes including ash lye solution, pH were consistently higher during fermentation (pH 8.6-8.9), and the number of isolated B. cereus sensu lato were lower.