The floodplain of the Amazon River is a large source for the greenhouse gas methane, but the soil microbial communities and processes involved are little known. We studied the structure and function of the methanogenic microbial communities in soils across different inundation regimes in the Cunia Reserve, encompassing nonflooded forest soil (dry forest), occasionally flooded Igapo soils (dry Igapo), long time flooded Igapo soils (wet Igapo) and sediments from Igarape streams (Igarape). We also investigated a Transect (four sites) from the water shoreline into the dry forest. The potential and resilience of the CH4 production process were studied in the original soil samples upon anaerobic incubation and again after artificial desiccation and rewetting. Bacterial and archaeal 16S rRNA genes and methanogenic mcrA were always present in the soils, except in dry forest soils where mcrA increased only upon anaerobic incubation. NMDS analysis showed a clear effect of desiccation and rewetting treatments on both bacterial and archaeal communities. However, the effects of the different sites were less pronounced, with the exception of Igarape. After anaerobic incubation, methanogenic taxa became more abundant among the Archaea, while there was only little change among the Bacteria. Contribution of hydrogenotrophic methanogenesis was usually around 40%. After desiccation and rewetting, we found that Firmicutes, Methanocellales and Methanosarcinaceae became the dominant taxa, but rates and pathways of CH4 production stayed similar. Such change was also observed in soils from the Transects. The results indicate that microbial community structures of Amazonian soils will in general be strongly affected by flooding and drainage events, while differences between specific field sites will be comparatively minor.