We investigated the Fe (Ⅲ) reduction capacity and the responses of Geobacteraceae spp. and Anaeromyxobacter spp. to 12-hour flooding, in terms of their 16S rRNA copy numbers, in five different paddy soils from four rice planting areas. We also studied the correlation between variations in abundance of Geobacteraceae spp. and Anaeromyxobacter spp. and microbial Fe (Ⅲ) reduction in soils of Jilin and Sichuan. The abundances of Geobacteraceae spp. and Anaeromyxobacter spp. were defined as the proportions of their 16S rRNA copy numbers to the bacterial count. Water logging was simulated and slurry samples were taken at 0 hours, 12 hours, 1 day, 3 days, 5 days, 7 days, 11 days, and 17 days. The results indicated that Fe (Ⅲ) reduction potential varied in different paddy soils and could be ranked in decreasing order as Jilin (5.18 g/kg), Tianjin (4.40 mg/g), Sichuan (3.40 mg/g), Zhejiang (3.07 mg/g), and Guangxi (1.86 mg/g). Thus, there appeared to be a declining trend that correlated with their geographical distributions from the north to the south. Geobacteraceae spp. and Anaeromyxobacter spp. in Jilin and Guangxi soils showed no sensitivity to 12-h flooding; however, Geobacteraceae spp. and Anaeromyxobacter spp. were sensitive to flooding in the soils of Zhejiang and Tianjin. Geobacteraceae spp. showed high sensitivity to flooding in Sichuan soil. During this short-term (17 day) incubation, the 16S rDNA copy number of Geobacteraceae spp. was on average significantly higher than that of Anaeromyxobacter spp. Thus Geobacteraceae spp. made a greater contribution to the overall Fe (Ⅲ) reduction compared with Anaeromyxobacter spp. The 16S rDNA copy numbers of both of these iron reducers reached their peaks at 11 days and fell to 20.0% (Geobacteraceae spp.) and 4.1% (Anaeromyxobacter spp.) of the level observed at day 11, after incubation for 17 days. Meanwhile, after 1 day of incubation in flooding conditions, the numbers of Geobacteraceae spp. were static, whereas the numbers of Anaeromyxobacter spp. decreased. After day 1, they accounted for just 0.1%-4.0% of the total bacteria, suggesting little contribution to Fe (Ⅲ) reduction at this stage. Notably, the abundance of Geobacteraceae spp. in Jilin soil was 38.3% on day 5, while the highest Fe (Ⅲ) reduction rate was observed on day 4, indicating the important role played by Geobacteraceae spp. in Fe (Ⅲ) reduction at this stage. The numbers of Geobacteraceae spp. and Anaeromyxobacter spp. in Jilin soil increased slowly from day 5 to day 11, which coincided with the replacement of Fe (Ⅲ) with sulfate as the electron accepter from 5 days after flooding. Geobacteraceae spp. and Anaeromyxobacter spp. both showed low abundance in the flooding soil of Sichuan, indicating that other, more abundant microbes were responsible for facultative Fe (Ⅲ) reduction and that these other microbes might be more worthy of further study. Euclidean distance clustering showed that the abundances of Geobacteraceae spp. and Anaeromyxobacter spp. in different soils after flooding of 0 hours and 12 hours could reflect the differences in their capacities for Fe (Ⅲ) reduction. The results demonstrated that the type of soil, its property, the planting area, and the variations in abundances of Geobacteraceae spp. in the different soils were closely related to the capacity for microbial Fe (Ⅲ) reduction in flooded paddy soils.