During Paleogene the Neotropical region was mainly covered by rainforests and ancient Amazon (AM) and Atlantic Forest (AF) were continuous and interconnected. The Andean uplift and drastic climate changes along the Eocene/Miocene resulted in the formation of a drier area separating AM from AF. However, multiple evidences have indicated recurrent connections between Neotropical rainforests during Quaternary. In this study we predict biogeographical connections between Neotropical Forests during the last glacial maximum (LGM—21 ka) and establish the climatic conditions that favored such connections. We tested if the general climatic conditions suitable to both Amazon (AM) and AF were uniform across current Cerrado and Caatinga areas or did subsets of these climatic spaces have independent spatial displacements connecting specific regions of AM and AF. For these, 50 occurrence points equidistant in the climatic space were sampled along the western and eastern AM and northern and southern AF and used to built ecological niche models (ENM) for each region. Potential distributions were predicted for the current and the LGM climatic scenarios using an ensemble approach. The ENMs detected the disjunct distribution of the two Neotropical rainforests in the present and showed three