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The ornamental plant stock flower (Matthiola incana (L.) R. Br.) has been widely cultivated in China. In 2021, stem rot on M. incana , which caused plant death, was first observed in Shanghai, China. Field surveys indicated a disease incidence of 15%–20%. Following pathogen isolation, identification was performed by combining morphological observation of colonies, sclerotia and apothecia, with molecular methods, including DNA sequencing and phylogenetic analysis. Morphological characteristics of the isolates, including white cottony mycelium, blackish globular to irregularly shaped sclerotia and apothecia formation, were consistent with Sclerotinia sclerotiorum. Results of sequence comparison and phylogenetic analysis based on the internal transcribed spacer (ITS) sequences supported morphological data. Pathogenicity assays were conducted successfully according to Koch's postulates. Considering the results of the morphological and molecular identification, along with the pathogenicity assessment, S. sclerotiorum was confirmed as the causal agent of stem rot of stock flower in Shanghai, China. A combination of cultural practices, rotation of resistant ornamentals, and biological and chemical treatments is recommended to control stem rot of stock. • Matthiola incana was susceptible to Sclerotinia sclerotiorum. • Pathogen was identified as S. sclerotiorum by morphological and molecular methods. • This is the first report of S. sclerotiorum causing stem rot of M. incana in China. • An integrated approach to the management of stem rot is recommended. [ABSTRACT FROM AUTHOR]