The boreotropical flora concept suggests that relictual tropical disjunctions between Asia and the Americas are a result of the expansion of the circumboreal tropical flora from the middle to the close of the Eocene. Subsequently, temperate species diverged at high latitudes and migrated to other continents. To test this concept, we conducted a molecular phylogenetic analysis (using cpDNA) of the Magnoliaceae, a former boreotropical element that currently contains both tropical and temperate disjuncts. Divergence times of the clades were estimated using sequences of matK and two intergenic regions consisting of psbA-trnH and atpB-rbcL. Results indicate the tropical American section Talauma branched first, followed by the tropical Asian clade and the West Indies clade. Within the remaining taxa, two temperate disjunctions were formed. Assuming the temperate disjunction of Magnolia acuminata and Asian relatives occurred 25 mya (late Oligocene; based on seed fossil records), section Talauma diverged 42 mya (mid-Eocene), and tropical Asian and the West Indies clades 36 mya (late Eocene). These events correlate with cooling temperatures during the middle to late Eocene and probably caused the tropical disjunctions.