The ability to quickly obtain accurate genome sequences of eukaryotic pathogens at low costs provides a tremendous opportunity to identify novel targets for therapeutics, develop pesticides with increased target specificity and breed for resistance in food crops. Here, we present the first report of the ~54 MB eukaryotic genome sequence of Rhizoctonia solani, an important pathogenic fungal species of maize, using nanopore technology. Moreover, we show that optimizing the strategy for wet-lab procedures aimed to isolate high quality and ultra-pure high molecular weight (HMW) DNA results in increased read length distribution and thereby allowing generation of the most contiguous genome assembly for R. solani to date. We further determined sequencing accuracy and compared the assembly to short-read technologies. With the current sequencing technology and bioinformatics tool set, we are able to deliver an eukaryotic fungal genome at low cost within a week. With further improvements of the sequencing technology and increased throughput of the PromethION sequencer we aim to generate near-finished assemblies of large and repetitive plant genomes and cost-efficiently perform de novo sequencing of large collections of microbial pathogens and the microbial communities that surround our crops.