traditional and rudimentary fermented foods and beverages especially those prepared from substrates rich in fermentable carbohydrates such as cassava peanuts and cereals contain a large number of microorganisms are responsible for the physical and chemical changes of these products in the case of the indigenous fermented beverage made with cotton seed and rice a large number of microorganisms were isolated and most were bacteria We used culture dependent and independent methods to determine the diversity of the bacteria and yeast found in the beverage naturally fermented with cotton seed and rice Using these methods we found that the lactobacillus and bacillus species were the dominant bacterial groups Representatives of the Corynebacterium and Enterobacteriaceae groups were found but not until the end of the fermentation process DGGE was not able to detect the corynecacterium species which may be due to the primer pair used in the PCR or the conditions for DGGE