Polyfluorinated 2-benzylthiobenzothiazoles 3a-l are prepared via a microwave-assisted, one-pot procedure. The advantages, such as good to excellent yields, shorter reaction time (14-21min), readily available starting material, and simple purification procedure, distinguish the present protocol from other existing methods used for the synthesis of 2-benzylthiobenzothiazoles. Bioassay indicated that most of the compounds showed significant fungicidal activity against Rhizoctonia solani, Botrytis cinereapers, and Dothiorella gregaria at a dosage of 50microg/mL. Interestingly, compared to the control of commercial fungicide, triadimefon, compound 3c exhibited much higher activities against R. solani, B. cinereapers, and D. gregaria, which showed that the polyfluorinated 2-benzylthiobenzothiazoles can be used as lead compound for developing novel fungicides.