Sclerotinia sclerotiorum, a notorious phytopathogenic fungus, causes sclerotinia stem rot in oilseed rape (Brassica napus), a disease with global consequences for oilseed rape productivity and oil quality. The complexity of factors contributing to sclerotinia stem rot makes prediction and control exceedingly challenging. Early and accurate identification of plant pathogens is crucial for effective disease management. This study aimed to establish a method utilizing MinION nanopore sequencing for identifying S. sclerotiorum and other fungi causing diseases in oilseed rape. Naturally infected leaf, soil and air samples were collected from oilseed rape fields in Sweden, and DNA was extracted. Two primer pairs targeting the ITS region known marker for fungus identification, were amplified by PCR. For nanopore sequencing, six PCR amplicon samples, two from each source were selected based on their purity and stem rot incidences, with one sample spiked-in with gDNA S. sclerotiorum as positive control. Bioinformatic analysis was performed using the CCMetagen tool and EPI2ME. Ascomycota and Basidiomycota constituted 34% and 45%, respectively, of the identified species. S. sclerotiorum was only detected in air field samples, and several other fungal species harmful to oilseed rape production in Sweden, such as Botrytis cinerea, Pyrenopeziza brassicae and many more, were identified. In conclusion, successful identification of plant pathogens, including S. sclerotiorum, was achieved using MinION nanopore sequencer.