Methanogens are widely distributed in anaerobic environment, such as flooded paddy soils, and are of vital importance in global carbon cycling, climate change and clean energy utilization. Previous studies found that microbial reduction of iron oxides, which are the most abundant oxides in paddy soils, could inhibit methanogenesis as ferric iron acts as a competitive electron acceptor. However, the effects of iron oxides on methanogens communities are less reported. By anaerobic incubation experiments added with formate only (control, CK) and both formate and ferrihydrite (Fh treatment), combined with 16S rRNA gene sequencing technique, we explored the changes of archaea communities induced by iron oxides in flooded paddy soil. Our results showed that compared to CK, adding ferrihydrite significantly reduced the proportion of archaea in total microbial community after incubation. At the operational taxonomic unit (OTU) level, a total of 21 OTUs were found at the end of incubation, 15 of which were detected both in CK and Fh treatments. Meanwhile, the addition of formate induced a lower shannon index and a higher simpson index of archaea community, indicating that the species richness and evenness were reduced. OTU 2056 and OTU 911 were enriched significantly, becoming the dominant and occupying 76%-80% in whole archaea communities, but the relative abundance of other OTUs decreased. However, the addition of ferrihydrite had no significant effect on the alpha diversity (shannon index and simpson index) and dominant strains. By means of phylogenetic tree analysis, OTU 2056 and OTU 911 had a close affinity with Methanobacterium bryantii which has been reported as hydrogenotrophic methanogens that could utilize formate. It thus indicates that iron oxides may only reduce the release of methane by inhibiting the growth of methanogens, but have no selective effect on the strains that act as the key role. This study helps to lay a foundation for exploring the microbial coupling of iron reduction and carbon cycling in soils.