Rapeseed is a versatile crop with significant economic value as fuel, food, and feed, contributing to farmers' income. However, its cultivation is often hindered by the devastating plant pathogen Sclerotinia sclerotiorum, which infects numerous plant species, including rapeseed. Stem rot disease caused by this fungus has historically caused substantial yield losses, ranging from 30 to 70% in Sweden, Germany, and the UK. The absence of disease-resistant cultivars poses a challenge for effective disease control. A real-time PCR is one of the several techniques used in laboratory for the detection of infection which has many benefits over conventional methods. But this study aimed to develop a technique for the detection of disease by confirming if MinION Nanopore Sequencing can be used for such purpose to save time, resources, and the environment as compared to real-time PCR and other conventional methods. Rapeseed leaves samples were collected from three naturally infested fields in Skaraborg; DNA was extracted and ITS regions which are commonly used marker or barcodes for identification of fungi were amplified with three different pair of primers. Amplicons were sequenced with MinION and hundreds of thousands of reads were recovered to Ascomycota and Basidiomycota fungi division while Saccharomycodes ludwigii fungi was the most abundant species recovered. Many pathogens were successfully detected while no single read of S. sclerotiorum could be recovered in the study. MinION is concluded to provide a fast and efficient method for the detection of plant pathogens however, in this study S. sclerotiorum were unable to be identified.