Botrytis aclada and Botrytis allii, associated with onion gray-mold neck rot and isolated in Hokkaido, were tested for sensitivity to benzimidazole. Of the B. aclada strains, 59% were highly resistant and the remaining 41% were sensitive; all strains of B. allii were sensitive. Resistant strains were widespread in Hokkaido. We analyzed the sequences of the beta-tubulin gene of resistant strains and detected the replacement of glutamic acid (GAG) by lysine (AAG) at codon 198. This is the first report of benzimidazole resistance in B. aclada. This study revealed a difference in fungicide sensitivity between the two Botrytis species.