To understand the dominant decaying microorganism, micro?ora composition and pollution pathways that causing gluten food deterioration, multiple samples of gluten foods were collected from various approaches, such as the factory production lines, large supermarket and small store. The total aerobic bacterial count, number of moulds and yeasts, coliforms and heat–resistance bacteria were tested using plate count method; the dominant microorganism were jointly isolated using plate streak method and point planting method, and their identification were based on the microscopic examination, physiological & biochemical test and the 16S rDNA gene sequence (the ITS sequence of 18S rDNA). The results showed that the total aerobic plate count from small store was 8×104 CFU/g, the number of moulds and yeasts reached to 1.20×103 CFU/g, which exceeded several times more than the limitation of local standard, while, the microbial populations from other sources of samples were in the scope of local standard. These results indicated that the extrusion technology was good for sterilization, but the later production and sale process was the main pathway leading to gluten food pollution. There 12 strains of bacteria which were subdivided into two categories and 8 strains of moulds which were subdivided into three categories were isolated in the test. The 2 dominant strains of bacteria were Psychrobacter faecalis, Pseudomonas fulva, and the 3 dominant strains of moulds were Asperqillus tamarii, Penicilium griseofulvum and Asperqillus niger.