BACKGROUNDGarlic leaf spot (GLS) caused by Alternaria alternata is one of the main diseases in the garlic production areas, and its management heavily relies on dicarboximide fungicides. However, the efficacy of dicarboximides against the GLS disease decreased year by year.RESULTSIn the study, 10 of 148 A. alternata strains separated from Jiangsu Province were moderately resistant (MR) to a dicarboximide fungicide procymidone (ProMR). Positive cross‐resistance was observed between procymidone and iprodione or fludioxonil, but not between procymidone and fluazinam or azoxystrobin. Mutations at AaOS1, but not Aafhk1, were confirmed to confer the procymidone resistance by constructing replacement mutants, whereas mutations at both AaOS1 and Aafhk1 decreased the gene expression level of AapksI, as well as the ability to produce mycotoxin AOH (polyketide‐derived alternariol) and virulence. And, more genes (AaOS1 and Aafhk1) harboring the mutations experienced more biological fitness penalty.CONCLUSIONTo our knowledge, this is the firstly report about the Pro‐resistance selected in the garlic fields, and mutations at AaOS1 of A. alternata causing the decreased ability to produce the mycotoxin AOH.This article is protected by copyright. All rights reserved.