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Abstract Previously, a boronium salt possessing a terminal benzyl group was reported to have greater antibacterial activity than a commercial quaternary ammonium disinfectant solution againstEscherichia coli,Pseudomonas aeruginosa, andStaphylococcus aureus. Results of the current study indicate that the same boronium salt without a benzyl group, exhibited equal or better antifungal activity against actively growingCandida albicansyeast andAspergillus fumigatusmold when compared to the same quat disinfectant. This same compound also displayed antifungal activity against dormantA. fumigatusspores comparable to the quat disinfectant. In contrast, the boronium ion with a benzyl group was 4–16X less effective than either the non‐benzylated form or quat disinfectant for all 3 fungal test conditions. The observation that the boronium salt without a benzyl group exhibited substantial antifungal activity in the current study but did not display any antibacterial activity in the previous study is of particular interest. This finding represents a flip‐flop outcome from the previous bacterial testing. It suggests that the presence of a terminal benzyl group greatly influences the boronium ion's ability to interact with fungal membranes.