The diversity and succession of bacteria during the natural fermentation of lima bean (Phaseolus lunatus) to produce daddawa (a fermented condiment) was studied using molecular method (16SrRNA gene analysis) with a view to develop a framework for production of daddawa of consistence quality with starter culture of Bacillus species. Lima bean was fermented for 72 h, during which isolation of bacteria and extraction of DNA were carried out. The extracted DNA of the bacterial isolates was tested for quality using agarose gel electrophoresis. The results of the 16SrRNA gene analysis were matched with the existing similar sequences in data base. Twenty six (26) presumptive isolates of Bacillus obtained at 24 h interval during the natural fermentation process were identified. The result of the ratio of absorbances of the extracted DNA at 260 and 280 nm showed that 73% of the isolates had pure DNA while the result of the gel electrophoresis showed well defined bands of the amplicons for the isolates. The BLAST result identified the isolates as Bacillus amyloliquefaciens, B. subtilis, B. pumilus, B. cereus and B. anthrasis with B. subtilis been the most predominant. Bacillus amyloliquefaciens, B. subtilis and B. pumilus occurred through-out the fermentation process. The study established the identity of the important Bacillus species involved in fermentation of lima bean into daddawa using molecular technique. These major Bacillus species could further be tested and developed as potential starters for improved production of daddawa from lima bean.