ABSTRACT Background The remarkable floristic diversity of the Atlantic Forest is partly related to the diversity of environmental conditions across its vast geographic extent that has resulted in distinct plant communities. Four areas (Pernambuco, Bahia and Northern Espírito Santo, São Paulo, and Araguaia-Tocantins refugia) have been hypothesised to have particularly high modern diversity due to their being located in areas of multi-millennial climate stability. Aims To test if species persistence and climatic stability over the last 21,000 years can predict hypothesised refugia in the Atlantic Forest domain. Methods We modelled the distributions of 282 tree species from various habitats and projected them using eight past climate scenarios in the last c. 21000 years. Based on the spatial overlaps among these projections, we inferred three types of refugia: species persistence refugium based on probability of occurrence, climatic stability refugium based on climate suitability and bioclimatic refugium based on the intersection of the previous two. We validated model projections with fossil pollen data. Results We identified five potential bioclimatic refugia (Bahia and Northern Espírito Santo, São Paulo, Paranaíba, Serra do Espinhaço and Subtropical Serra do Mar) and one climatic stability refugium (Pernambuco). Conclusions We validated three of four previously hypothesised refugia and detected two additional ones by considering both species persistence and climatic stability as key determinants of refugia.