Understanding the nature and extent of ecosystem boundaries has important implications for the management and conservation of biodiversity. However, characterizing and establishing such boundary limits has been a persistent challenge worldwide. The Cerrado–Amazonia transition (CAT) in Brazil is the world’s largest savanna-forest transition. However, the CAT is represented in official maps used by Brazilian governmental agencies as a simple line separating the two biomes. Here, we demonstrate that the CAT is in fact broad, complex and interdigitating and that its traditional linear representation is not adequate for recognizing and conserving biodiversity in this region. Over the 30 years of our analysis, the CAT suffered more deforestation than the forests and savannas in each individual biomes (Amazonia and Cerrado). The complexity of tropical savanna-forest boundaries has been misunderstood and misrepresented by current maps, severely threatening the complex CAT biota. As a consequence, vegetation losses have reached levels close to collapse in areas of intense human activity.