Most natural and synthetic dyes currently used for microbial fluorescent staining are toxic or carcinogenic and are harmful to animals, humans and the environment. A food dye for microbial staining, brilliant blue FCF, was used as an alternative to lactofuchsin and lactophenol blue. Brilliant blue FCF shows pronounced microbial cell fluorescence staining of an array of pathogenic/toxigenic (Fusarium granunearum 3- and 15-acetyldeoxynivalenol chemotypes, and Escherichia coli O157:H7) and beneficial fungi and bacteria (Trichoderma harzianum and Bacillus subtilis). Brilliant blue FCF has no toxic effects on the microbes tested and is inexpensive.