The methanogen flora of soil samples taken from nine paddy fields in Japan was analyzed. Archaeobacterial 16S-ribosomal DNA (positions 1112 to 1379 in the Escherichia coli numbering system) was amplified from DNA extracted directly from soil samples using PCR. The amplified DNA was cloned into the bluescript SK+ phagemid vector, and approximately 100 clones (10–30 clones for each soil sample) were sequenced. The composition of methanogen flora was deduced from ratios of the clones which were identified to genus level based on their sequences. Methanosarcina-like clones (which made up 55% of the total number of methanogen clones) were predominant in most of the soil samples. Methanogenium-like and Methanosaeta-like clones predominated in some soil samples, making up 25% and 17% of the total number of methanogen clones respectively. Individual clones were compared and identified in detail by calculating sequence similarities. All the Methanosarcina-like clones demonstrated sequences which were mostly identical to Methanosarcina mazei, and all of the Methanosaeta-like clones demonstrated sequences similar to Methanosaeta concilii. Less similarity was observed between the sequences of Methanogenium-like clones and those of Methanogenium and Methanoculleus, indicating that novel Methanogenium-like organisms exist in these soils as major methanogens.