Genome of a culture with very slow growth and low yield. DNA was amplified by MDA (RepliPHI kit) prior to sequencing. Sequencing was done with Illuminia MiSeq (PE150), assembly was done with A5-miseq. The genome was manually curated to a circular chromosome in Geneious 7.1.7 by repeated rounds of read mapping, primer design for contig ends and low-coverage regions and sanger sequencing of PCR amplicons. 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.