Ancient irrigated paddy soils from the Neolithic age of 6280 a BP and Shang-Zhou Period of 3320 a were excavated at Chuo-dun-shan in the Yangtze River Delta, close to Suzhou, Jiangsu Province of China. The objective of this study was to carry out a survey of the bacterial, archaeal and methanogenic archaeal community diversities in these soils under different rice farming practices. PCR-DGGE analyses of V3 regions of 16S rDNA gene fragments were employed to profile community diversities in different soil layers. These included Neolithic, Shangzhou and present day paddy soils collected between 100-116, 42-57, 0-15 cm′s respectively from the soil surface. In addition parent material (174-200 cm) was also sampled. The results show that clear molecular finger-printings in ancient irrigated paddy soils were gained using PCR-DGGE. The DGGE band patterns differed between paddy soil types, and exhibited more diverse DGGE band patterns compared with the parent material. UPGAMA analyses concurred with the DGGE results and showed that bacterial, archaeal and methanogenic archaeal communities were separated from present paddy soil, Shang-Zhou paddy soil, Neolithic paddy soil, and parent material. Based on our findings we concluded that the buried ancient irrigated paddy soils still have a large number of bacteria, archaea and methanogenic archaea surviving. The rice farming practices increased diversity in present day, Shang-Zhou and Neolithic paddy soils compared with the parent material. The different rice farming practices might induce specific community development, and different rice farming practices probably led different predominant species in the irrigated paddy soils.