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Brazil has high levels of biodiversity and has received strong criticism for the increasing country-wide deforestation that threatens it. Although a significant percentage of land area in Brazil is protected, the areas are insufficient and unevenly distributed. Many studies have contributed to the biogeographical knowledge of Brazilian flora, but no endemicity analysis (EA) has been conducted including all endemic angiosperms. We investigated the spatial component, drawing on a huge and taxonomically diverse dataset based on 827 016 records collected over the last two centuries. We conducted an EA for 15 034 species from 173 families using an optimality criterion with 2° and 3° grid sizes, in order to search for distributional concordance, to identify the biogeographical units and discuss the implications for conservation. Six analyses were run for basal angiosperms, monocots and eudicots. The EA recovered 66 consensus areas (CAs). The concordance of CAs enabled the identification of five best-supported areas of endemism--three in the Atlantic and Parana Forest and two areas in the Cerrado province--supported by species of 120 families. The age of divergence for some genera that contributed significantly to the identification of areas recovered in the Cerrado coincides with the recent, <10 Ma, estimated age of that province. By contrast, the areas in the Atlantic and Parana Forest are supported by genera with earlier diversification >30 Ma, supporting an ancient origin. Most areas in the Atlantic Forest are partially superimposed with the limits of the protected areas, however, big gaps were identified in the Cerrado. Protecting Brazilian biomes was at the heart of Brazil's environmental policy. Regrettably, this scenario has radically changed based on misleading divergences in conservation policy. Areas of endemism are pivotal for biodiversity conservation due to the common evolutionary history shared by their endemic taxa. Thus, we hope that these congruent patterns of endemism support the establishment of biodiversity priorities.