Bacteria are an important compatible group of microorganisms which live within insect gut. Most of these microorganisms are useful to help the digestive system to work better. The aim of this study was to identify the symbionts bacteria associated with Plodia interpunctella and Ephestia kuehniella guts to use in future biotechnology studies. The larva from the two above-mentioned insects wereprepared and their guts organ were used to isolate symbiotic bacteria. The bacteria were isolated and purified on the enriched nutrient agar medium and their frequency was recorded. Based on the phenotypic characteristics the isolated bacteria were preliminary characterized. Then after comparing of their total soluble proteins by electrophoresis, they were kept for further studies. Identification of bacteria were done based on phenotypic characteristics with standard bacteriological methods as well as use of 16SrRNA encoding gene sequence and its comparison with NCBI data bank. Results indicated that the dominant symbiont bacteria in the Ephestia kuehniella gut were Bacillus toyonensis, Serratia marcescence and in Plodia interpunctella gut were Bacillus safensis, Bacillus zhangzhouensis and Bacillus wiedmannii. The accuracy of the results for phenotypic determination was verified by molecular analyzes using DNA sequences of the 16SrRNA gene comparission via NCBI sequences database. This is the first study on gut symbionts of Ephestia kuehniella and Plodia interpunctella in Iran.