For decades, palynologists working in tropical South America are using the genus Podocarpus as a climate indicator although without referring to any modern data concerning its distribution and limiting factors. With the aim to characterize the modern and past distribution of the southern conifer Podocarpus in Brazil and to obtain new information on the distribution of the Atlantic rainforest during the Quaternary, we examined herbarium data to locate the populations of three Brazilian endemic Podocarpus species: P. sellowii, P. lambertii, and P. brasiliensis, and extracted DNA from fresh leaves from 26 populations. Our conclusions are drawn in the light of the combination of these three disciplines: botany, palynology, and genetics. We find that the modern distribution of endemic Podocarpus populations shows that they are widely dispersed in eastern Brazil, from north to south and reveals that the expansion of Podocarpus recorded in single Amazonian pollen records may have come from either western or eastern populations. Genetic analysis enabled us to delimit regional expansion: between 5° and 15° S grouping northern and central populations of P. sellowii expanded c. 16,000 years ago; between 15° and 23° S populations of either P. lambertii or sellowii expanded at different times since at least the last glaciation; and between 23° and 30° S, P. lambertii appeared during the recent expansion of the Araucaria forest. The combination of botany, pollen, and molecular analysis proved to be a rapid tool for inferring distribution borders for sparse populations and their regional evolution within tropical ecosystems. Today the refugia of rainforest communities we identified are crucial hotspots to allow the Atlantic forest to survive under unfavourable climatic conditions and, as such, offer the only possible opportunity for this type of forest to expand in the event of a future climate change.