AbstractNaegleria fowleri is an environmental protist found in soil and warm freshwater sources worldwide and is known for its ability to infect humans and causing a rapid and mostly fatal primary amoebic meningoencephalitis. When contaminated water enters the nose, the facultative parasite follows the olfactory nerve and enters the brain by crossing the cribriform plate where it causes tissue damage and haemorrhagic necrosis. Although N. fowleri has been studied for several years, the mechanisms of pathogenicity are still poorly understood. Furthermore, there is a lack of knowledge on the genomic level and the current reference assembly is limited in contiguity. To improve the draft genome and to investigate pathogenicity factors, we sequenced the genome of N. fowleri using Oxford Nanopore Technology (ONT). Assembly and polishing of the long reads resulted in a high-quality draft genome whose N50 is 18 times higher than the previously published genome. The prediction of potentially secreted proteins revealed a large proportion of enzymes with a hydrolysing function, which could play an important role during the pathogenesis and account for the destructive nature of primary amoebic meningoencephalitis. The improved genome provides the basis for further investigation unravelling the biology and the pathogenic potential of N. fowleri.