Abstract: The bacterial and archaeal community structure and the influencing factors had been detected in paddy soils of super hybrid rice cultivation areas based on high throughput sequencing. Soil samples were collected from Longhui (HLW, high-yield) and Ningxiang (LNX, low-yield) at four different stages (pre-transplanting, tillering, booting and mature stage) with the cultivation of super hybrid rice “Y Liangyou 900”. Combined with the soil physiochemical properties, the main driving factors were analyzed. Results showed that the bacterial diversity during cultivation was significantly higher than that in pre-transplanting stage in high-yield area (P<0.05), and no significant difference among the four stages in low-yield area (P>0.05). The shared dominant phyla in both areas were Proteobacteria, Acidobacteria, Chloroflexi and Verrucomicrobia, whereas Bacteroidetes just dominated the high-yield area. The relative abundance of Chloroflexi in low-yield area was significantly higher than that in high-yield area (P<0.05), while the relative abundances of Bacteroidetes and Proteobacteria were much higher in high-yield area (P<0.05), and no significant differences of the relative abundances of Acidobacteria and Verrucomicrobia were detected between the two areas (P>0.05). The relative abundance of archaeal community in low-yield area was 2.8-5.5 times higher than that in high-yield area (P<0.05). The dominant phylum was Crenarchaeota in low-yield area, whereas Euryarchaeota dominated the high-yield area. The variations of relative abundances of Crenarchaeota, Euryarchaeota, Acidobacteria and Verrucomicrobia had the same trend with decreasing first and then increasing during the four stages, while the Chloroflexi had an opposite trend. The relative abundances of Bacteroidetes and Proteobacteria were declined through the four stages. RDA analysis indicated that soil organic matter was the most important environmental factor affecting Proteobacteria, while available P was the key factor influencing Bacteroidetes and Proteobacteria communities. The key driving factor in shaping microbial communities in high-yield and low-yield areas was available N and available P, respectively. In a word, the soil bacterial and archaeal communities was obviously different between high-yield and low-yield areas, and varied with the super hybrid rice growth stages. The results revealed that contents of available nutrients were the main factors affecting soil bacterial and archaeal communities.