Genome of a culture that was harvested by centrifugation; DNA was extracted with the Quiagen MagAttract HMW DNA kit. Sequencing was done with Illuminia MiSeq (PE250), trimming of reads with trimmomatic, assembly with SPAdes. The genome was manually polished in Geneious 9 by repeated rounds of read mapping. Completeness and contamination were assessed with CheckM, but as the genome consists of a circular chromosome, it should be complete without any contamination. We have meanwhile isolated and genome-sequenced many additional strains of Methylopumilus, all of these are complete (one circular chromosome) with low completeness estimated by CheckM, which might be caused by the streamlined genome of this genus.