Flowers of Magnoliaceae emit strong to moderate odors composed of various types of chemical compounds, usually present in distinctive combinations within taxa. Some temperate eastern Asian and North American species of Magnolia (disjuncts), however, have similar chemical profiles. A molecular phylogeny of Magnoliaceae was constructed to reveal phylogenetic relationships of taxa by sequencing the trnK intron (including the matK coding region), psbA-trnH, and atpB-rbcL intergenic spacer regions of chloroplast DNA from 25 Magnolia, two Michelia, and two Liriodendron taxa. The psbA-trnH spacer region showed twice the sequence divergence (0.0157) of the trnK intron (0.0073) or the matK coding region (0.0077). The strict consensus tree constructed from the combined data set (ca. 3,700 bp) indicated the genus Magnolia was polyphyletic containing Michelia species as ingroup. The clade of Magnolia liliifera var. obovata, M. coco, and M. delavayi formed the first branch. Among the remaining species, two additional large clades were recognized, i.e., one comprised of American evergreen Magnolia species and another of subgenus Yulania. The relationship among sect. Rytidospermum taxa was not clearly resolved. Parsimonious mapping of the floral scent chemical characters was performed onto the molecular phylogenetic tree to discuss evolutionary trends of the floral scent chemistries.