Biodiversity has gained international relevance with the Convention on Biological Diversity (CBD). An important signatory of the agreement, Brazil is a megadiverse country with vast biomes. Internally, the Brazilian federative organization is characterized by discrepancies between the jurisdictional scale and natural boundaries. From a governance perspective, this article analyzes how political administrative bodies deal with biome subsets, using the Atlantic Forest biome as reference. The problem was researched through the dynamics between scales and levels, considering the action of governmental and non‐governmental actors in the process, in the context of an adaptive approach. To overcome the mismatches between the federative structure and the biome, we present the ‘governance of scales’ model, which proposes articulation between the spatial scale and jurisdictional scale, through the institutional and management scales. Previous experiences of the Brazilian government in harmonizing watersheds and the coastal region with federalism enhance the feasibility of our biome‐level proposal. The model is a useful contribution to biodiversity governance in favor of novel arrangements to improve the fit between social and ecological systems. Copyright © 2016 John Wiley & Sons, Ltd and ERP Environment