A TaqMan/MGB probe PCR (polymerase chain reaction) technology can carry out bacterial genus identification on clostridium difficile in fecal genomes, simultaneously detect the carrying situation of toxin genes, and can judge whether a toxin A has deletion. A fecal specimen is not required to be purely cultured, and the strain identification and the toxin detection are completed in a reaction system. The method has the characteristics of simple operation, good repeatability, high flux detection specimens, short report time, and the like, and is applicable to the screening of pathogenesis of patients with diarrhea caused by clinically unexplained causes. The invention solves the technical problems that fecal specimens can be subjected to strain identification and strain toxin carrying situation screening simultaneously without being purely cultured, and a DNA (deoxyribonucleic acid) detection method for fecal genomes, which is high in sensibility, is provided. Because traditional anaerobic culture is uneasy to perform, and an enzyme immunoassay has methodology defects, according to the invention, the diagnosis rate of clostridium difficile associated diarrhea is significantly increased. Meanwhile, the invention also can be applied to the monitoring of drug used in the process of treating the diseases.