Flooded rice fields are a major source of atmospheric methane, a strong greenhouse gas second only to carbon dioxide. Rice roots are one of the most important hotspots for methane oxidation in rice fields. However, limited information is available on the physiological and genomic characteristics of methane-oxidizing bacteria (MOB) inhabiting rice roots. In the present study, we isolated MOB from rice roots and characterized the strains phenotypically and genomically. We obtained 100 MOB-enriched cultures from the roots of three rice cultivars (Oryza sativa L. subsp. japonica cv. Nipponbare, O. sativa L. subsp. indica cv. Muha, and Tupa 121-3), in which twelve MOB isolates, two Methylomonas sp., three Methylocystis sp., and seven Methylosinus sp., were successfully purified. They showed different morphological features (types of flagellation) and colony formation potentials within the same group in some cases. A genome sequencing ana­lysis revealed variations in the number of genes or the clusters of methane monooxygenase, methanol dehydrogenase, and nitrogenase. The number of plasmid DNAs also differed among the strains. Four strains belonging to the genus Methylomonas or Methylocystis represented putative novel species based on their phenotypic and genotypic characteristics. The present study largely expanded the eco-collection of MOB cultures inhabiting rice fields and rice roots.