Type genome is Methylopumilus rimovensis MMS-RI-1 (GCF_006364615.1), an axenic bacterial strain isolated by dilution-to-extinction cultivation from the water column of the Římov Reservoir (Czechia). MMS-RI-1 has a genome size of 1.28 Mb with a genomic GC content of 36.7%, contains 3 rRNA genes and 37 tRNAs. The genome is complete, consisting of 1 circular chromosome. Methylopumilus rimovensis are very small, aerobic, non-motile and methylotrophic. The genome contains genes encoding two rhodopsins (proteorhodopsin and xantho-like rhodopsin) and the biosynthetic pathway for retinal biosynthesis. No genes for flagellar or pilus assembly and chemotaxis were annotated. Pathways for methanol oxidation (Xox) and the RuMP cycle for methylotrophy and the biosynthesis of all amino acids were predicted. Methylopumilus rimovensis are highly abundant only in their isolation source (the Římov Reservoir in Czechia) and recorded in very low abundances in other freshwater lakes, which contrasts with members of other species of the genus that have a global distribution (Methylopumilus planktonicus and Methylopumilus universalis). None of the isolated strains were yet submitted to a culture collection because these bacteria are hard to maintain, i.e., they are very slowly growing, reach low densities in liquid culture, and do not grow on agar plates.