Vertical changes in bacterial and archaeal communities (mainly methanogen) with soil depth in three Japanese paddy fields (Tatsuta, Nagakute and Ichinomiya, Aichi prefecture) were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative PCR. All fields were located in an alluvial area and the soil texture differed among the layers. The Nagakute and Ichinomiya paddy fields were well-drained paddy fields (Gray Upland soil and Gray Lowland soil, respectively), whereas the Tatsuta paddy field was a wet paddy field (Gley soil). The amount of extracted DNA drastically decreased below a depth of 20 cm and remained at a low level in the deeper layers in all fields. Numbers of mcrA genes, encoding the methyl-coenzyme M reductase α subunit of methanogenic archaea, drastically decreased with depth in the Nagakute and Ichinomiya paddy fields; high numbers of mcrA genes were retained through the layers in the Tatsuta paddy field. Cluster analysis of the DGGE band patterns of the bacterial and archaeal communities showed that their patterns in each field were initially divided into two groups, upper and lower layers, except for the bacterial community in the Tatsuta paddy field. These differences in the communities roughly corresponded to the distribution of the rice roots. Sequencing analysis of representative DGGE bands of the archaeal communities showed that diverse methanogens belonging to members of Methanomicrobiales, Methanosarcina spp., Methanosaeta spp., Methanocellales and Methanobacteriaceae inhabited the plowed soil layer, whereas uncultured members in the cluster ZC-I group of Methanosarcinales were more predominant beneath the plowed soil layer. Archaeal members other than methanogens inhabited the deeper layers of the Nagakute and Ichinomiya paddy fields. These results showed that the populations and compositions of bacterial and archaeal communities in paddy fields distinctly varied with soil depth, and indicated that the distribution of rice roots and the groundwater level might affect the populations and compositions in the subsoil.