A coliform flora analysis method using real-time polymerase chain reaction (PCR) was developed. The amplified region targeted was lacZ , encoding β -galactosidase. Forty-two species belonging to 16 genera of coliform bacteria were successfully detected. Specific primers were designed to detect the genus Klebsiella / Enterobacter and the genus Citrobacter , allowing for the discrimination of coliform bacteria into 3 groups. Quantification of bacterial numbers ranged from 10³ to 10⁶ cfu per PCR reaction vessel. Differences in flora between vegetables and meat, and among various factory locations, were able to be detected. Finally, sources of contamination were investigated in a real food factory. Coliform bacteria were detected in 23 out of a total of 32 samples. As a result of cluster analysis, 4 potential sources of contamination during the manufacturing process were proposed for the 2 products. Analysis of the flora was completed in approximately 5 hours; thus, a rapid contamination source search system has been developed.