Prevalence of Bacillus cereus was determined in red pepper powder samples obtained from various processing steps (n=60), swabs of machinery surfaces (n=35), and air samples of the processing room (n=17) during red pepper powder production. The detection rate of B. cereus was high (over 85%) in samples of raw materials and washing steps and decreased to 40% in samples obtained from later stages of processing, i.e. milling, metal detection, and final products. B. cereus was detected in 2.9 and 11.8% of swabs and air samples, respectively. The genetic similarity of B. cereus isolates obtained from various processing steps was compared to identify the sources of contamination for red pepper powder using the repetitive-sequence-based polymerase chain reaction method. For 20 isolates of B. cereus from two independent samplings, 50% of the isolates, which were clustered, consisted of two or more isolates with a similarity greater than 95%. For the isolates obtained from raw materials, crude milling, and milling step of the independent sampling, high genetic similarity (>99.4%) was observed, suggesting that these isolates may have originated from the same clone. The prevalence of B. cereus and molecular typing result suggest possible routes of contamination, such as the transfer of clone contaminated in raw materials to the red pepper powder and cross contamination during processing. Based on this result, more intervention studies to prevent pathogen contamination during red pepper powder processing are needed to insure good hygienic level of products.