Introduction and Objectives Anaplasma phagocytophilum (Aph) is a strict intracellular bacterium transmitted by Ixodes spp. ticks. It infects humans, mainly in the USA, whereas in Europe, ruminants are strongly affected. Hosts and clinical signs are strain dependent. Genomes are too few on NCBI (33) and may have a questionable quality and completeness to identify genetic factors responsible for these differences. The lack of quality is hindered by the difficulty in isolating and cultivating Aph and separating Aph DNA from the vertebrate host genome. The goal of this project is to implement long read Oxford Nanopore Sequencing (ONS) to obtain more diverse genomes to compare them with those already published, for downstream applications such as phylogeny analysis, improvement of diagnosis. Material and Methods We performed ONS, which produces less fragmented genomes than short-read technology and increases genome completeness, on three samples: two Aph-infected cell cultures, with significantly higher Aph to host DNA ratios, and one blood sample from a naturally Aph-infected cow, with a low abundance of bacterial DNA. Sequencing results were filtered to eliminate host DNA and retain specific Aph sequences prior to assembly with Flye to obtain high-quality genomes. Assemblies were performed on subsampled reads at different coverage levels (10x to 100x) to evaluate the minimum number of reads required for high-quality genomes. Results, Discussion, and Conclusion For cultured samples, we obtained 88% and 30% Aph from total sequences, corresponding to a bacterial genome coverage exceeding 1000x. We found that at 20x coverage, assemblies had good quality with a median of 2 contigs, a genome size of 1.5 Mb, and a 41.66% GC content, like published reference genome. For the blood sample, the ratio of Aph to host DNA was much lower, with only 0.03% Aph sequences observed. Therefore, we will perform adaptive sampling, an ONS specific method that enriches or depletes samples during sequencing. It will help increase Aph sequences obtained from blood samples collected from different hosts and geographic locations. This will help to generate more Aph reference genomes and thus to elucidate its pathogenicity. It will also enable us to improve diagnostic sensitivity in infected animals and humans.