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Recent evidence has shown that most tropical species are declining as a result of global change. Under this scenario, the prevalence of tolerant species to disturbances has driven many biological communities towards biotic homogenization (BH). However, the mechanisms that drive communities towards BH are not yet thoroughly understood. We tested effects of recurring wildfires on woody species richness and composition in six seasonally flooded Amazonian forests and whether these fires reduce species composition (i.e., taxonomic homogenization) over short periods of time. Our results show that these forests are undergoing taxonomic homogenization in response to recurring fire events. Species richness decreased as a result of local extinctions and floristic similarity increased among forest communities. Fire was selecting tolerant (‘winner’) species and eliminating the more sensitive (‘loser’) species. BH leads to biodiversity erosion, which can deeply alter ecosystem processes such as productivity, nutrient cycling and decomposition, resulting in important consequences for conservation.