Oilseed rape is a crucial crop for vegetable oil, animal feed, and biodiesel production. Sclerotinia Stem Rot (SSR) is a disease caused by Sclerotinia sclerotiorum, and is one of the most economically damaging to oilseed rape. Traditional detection methods for this virulent phytopathogen are often time-consuming and labour-intensive. This study aimed to evaluate the efficiency of MinION Nanopore sequencing and CCMetagen 1.3 tool, for detecting Sclerotinia sclerotiorum in air samples from oilseed rape fields. In this study, air samples were collected weekly over six weeks from an SSR-infected field, and DNA was extracted from the weekly samples. The fungal internal transcriber spacer (ITS) region is recognized as a barcode for species identification. This fungal ITS region in the air samples DNA, was PCR amplified using primer pair ITS1catta and ITS4ngsUni, after determining optimal annealing temperature. Sequencing of the amplified ITS region was performed using both flow cell and flongle platforms on the MinION device, followed by data analyzed via the CCMetagen 1.3 tool for taxonomic classification. S. sclerotiorum was detected in all six weekly pooled air samples DNA, along with other oilseed rape pathogens like Albugo candida, Alternaria brassicae, Botrytis cinerea, Hyaloperonospora brassicae and H. parasitica, and Pyrenopeziza brassicae. The MinION Nanopore sequencing and CCMetagen 1.3 analysis method demonstrated high sensitivity, highlighting its potential for monitoring minute pathogen presence in agricultural settings. This method provides an effective and efficient alternative to traditional detection techniques, offering significant advantages for early disease detection and management in oilseed rape cultivation.