Nanopore sequencing is a novel technology which allows sequencing of entire genomes using a relatively cheap, handheld device – Oxford Nanopore’s MinION – powered by a state of the art personal computer. The technology generates long reads allowing for high quality genome assemblies while offering unmatched portability and simplicity of use. Here we aimed for sequencing the whole genome of an apple blossom isolate of Metschnikowia pulcherrima, with proven in vitro efficacy in controlling post-harvest fungal pathogens. Using five flow cells, 338MB of high quality sequence data was obtained allowing a de novo assembly of the 16MB genome of Metschnikowia pulcherrima to 21x coverage. The de novo assembly generated consists of 20 contigs of a N50 contig length of 1.23MB and shows a 98.17% consensus identity to the reference genome. Furthermore a polishing of the raw nanopore assembly using short and accurate Illumina reads resulted in an increase of this consensus identity to 99.45%. The data presented here shows that Nanopore sequencing allows for efficient and accurate sequencing of fungal genomes when combined with Illumina sequence data. While a de novo assembly shows promising results, the accuracy is not yet high enough. Nonetheless, we estimate that further improvements to the sequencing technology and better bioinformatic tools will allow such de novo sequencing of fungal genomes using only Nanopore sequencing data in the near future.