Extreme drought events, driven by the El Niño Southern Oscillation (ENSO), are linked to increased tree mortality and alterations in vegetation structure, dynamics, and floristic composition in tropical forests. Existing analyses, primarily focusing on Africa, Central America, and Amazonia, overlook the floristic impacts on biome transitions. This study evaluates the profound effects of the severe 2015/2016 ENSO event on tree density and floristic composition in the critical transition zone between Amazonia and Cerrado, South America's largest biomes. Our findings not only document significant biodiversity loss but also offer insights into species resilience, guiding conservation strategies under changing climate conditions. We inventoried long-term plots before and after the extreme drought event, sampling 12,465 individuals from 526 species, 224 genera, and 65 families, in Open Ombrophilous Forest (OF), Seasonal Forest (SF), Cerradão (CD), and Typical Cerrado (TC). We document the disappearance from our plots of 97 species after the ENSO, with only 61 new species being recorded. The total loss of individuals across the transition zone was almost 10 %. The SF and CD forest plots showed the greatest replacements, species losses, and reductions in tree density. Their markedly seasonal baseline climate probably drove these changes. In most phytophysiognomies, there was an increase in pioneer species and drier environment habitat specialist species, indicating that although many species are vulnerable to extreme climate events, others benefit, especially those with a short life cycle. We found that the vegetation of the Amazonia-Cerrado transition overall is vulnerable to climate anomalies, with widespread loss of tree density and change in floristic composition. Our study also provides a species-by-species list of the most vulnerable and resistant trees which helps point to overall climate change vulnerabilities and assist with initiatives to recover degraded areas.