Auricularia polytricha is an important edible and medicinal fungus in Taiwan. The cultivation environment and sterilization of the mushroom cultivation bag before cultivation may affect the fungal species that occur along the fruiting body for Mucor irregularis, M. fusiformis, and Trichoderma longibrachiatum and the stalk, for Hypocrea koningii, Rhodotorula mucilaginosa, and Coprinellus radians from the stalk. The bacterial species associated with A. polytricha were also identified by PCR amplification, PCR-RFLP analysis, sequencing and BLASTn analysis. Bacterial species were identified as Bacillus cereus, Pseudomonas tolaasii, Sphingomonas paucimobilis, Acinetobacter pittii, and Lysinibacillus fusiformis in the homogenates after Pasteur sterilization. During a flavor test of 11 commercial drinks, the testers reported experiencing diarrhea. Bacterial examination of the drinks found that three samples were contaminated. Five bacterial species were identified as Pantoea agglomerans, Serratia liquefaciens, and Pseudomonas psychrophila in sample 275, Cronobacter sakazakii and Pseudomonas azotoformans in sample 684 and Pseudomonas azotoformans in sample 539, and more than one bacterial species occurred in two samples. In conclusion, pathogenic fungal and bacterial species were obtained from the fruiting bodies, stalks, homogenates, and drinks of A. polytricha after Pasteur sterilization. To prevent foodborne diseases from A. polytricha, sanitation procedures should be enforced during cultivation, processing and post-harvest storage.