The two major rainforests of the neotropics, the Amazon and Atlantic forests, show maximum expansion during the warm and wet conditions of interglacial periods, including the current Holocene. They are connected by a network of gallery forests through the Cerrado biome. However, the extent of their expansion during glacial periods, when they were more disjunct, is unknown. During glacial periods, a pollen assemblage comprising Podocarpus–Ilex–Hedyosmum–Myrsine displays higher frequencies in marine, continental and coastal Brazilian pollen records. This assemblage is observed today in the high-elevation grasslands of the Cerrado and Atlantic Forest biomes and in the coastal vegetation, the restinga, of southern Brazil. We therefore reviewed the possible migration routes for these species by tracking glacial period Podocarpus–Ilex–Hedyosmum–Myrsine assemblages in published pollen records. The marine pollen records provide evidence of a glacial expansion of restinga, its floristic composition being continuous with the dominant regional vegetation, a cold type of shrubby grassland. There appear to be two migration routes, one involving the expansion of high-elevation grassland taxa within the lowlands, and the other low-sea level stands of coastal restinga. We conclude that the Cerrado was a node of migration between the Amazon and Atlantic rainforests, linking the Andes to the central and coastal mountains of Brazil. The Brazilian mountain ranges represent refugia of ancient taxa that colonized the continent up to the Andes and modified the floristic composition of the two rainforests during the Pleistocene glacial periods.