Studies addressing microbial biogeography haveincreased during the past decade, but research onmicrobial distribution patterns is still in its infancies,and many aspects are only poorly understood. Here,we compared the methanotroph community in paddysoils sampled in Indonesia, Vietnam, China and Italy,focusing on the distance–decay relationship.We usedthe pmoA gene as marker for methanotroph diversityin terminal restriction fragment length polymorphism,microarray and pyrosequencing approaches. Wecould observe a significant increase of β-diversity with geographical distance across continents (12 000 km).Measured environmental parameters explained only asmall amount of data variation, and we found no evidencefor dispersal limitation. Thus, we propose historicalcontingencies being responsible for theobserved patterns. Furthermore, we performed anin-depth analysis of type II methanotroph pmoA distributionat the sequence level. We used ordinationanalysis to project sequence dissimilarities into athree-dimensional space (multidimensional scaling).The ordination suggests that type II methanotrophs inpaddy fields can be divided into five major groups.However, these groups were found to be distributed inall soils independent of the geographic origin. Byincluding tropical field sites (Indonesia and Vietnam)into the analysis, we further observed the firstpaddy fields harbouring a methanotroph communitydepleted in type II methanotrophs.