The complete genome of a model obligate methylotroph, M. flagellatus (strain KT) was sequenced. The genome is represented by a single circular chromosome of approximately 3 Mbp potentially encoding a total of 2,766 proteins. Based on genome analysis as well as the results from previous genetic and mutational analyses, methylotrophy is enabled by methanol- and methylamine dehydrogenases, the tetrahydromethanopterin-linked formaldehyde oxidation pathway, the assimilatory and dissimilatory branches of the ribulose monophosphate cycle, and a formate dehydrogenase. Some of the methylotrophy genes are present in more than one (identical or non-identical) copy. The obligate dependence on single carbon compounds is likely due to the incomplete tricarboxylic acid cycle, as no genes potentially encoding alphaketoglutarate-, malate- or succinate dehydrogenases are identifiable. The genome of M. flagellatus was compared, in terms of methylotrophy functions, to the previously sequenced genomes of three methylotrophs: Methylobacterium extorquens (Alphaproteobacterium, 7 Mbp), Methylibium petroleophilum (Betaproteobacterium, 4 Mbp), and Methylococcus capsulatus (Gammaproteobacterium, 3.3 Mbp). Strikingly, metabolically and/or phylogenetically, methylotrophy functions in M. flagellatus are more similar to the ones in M. capsulatus and M. extorquens than to the ones in the more closely related M. petroleophilum, providing the first genomic evidence of polyphyletic origin of methylotrophy in Betaproteobacteria.