Section Macrantha is a monophyletic group with 18–22 species, all of which are distributed in Asia except for Acer pensylvanicum in eastern North America. Nuclear sequences from nrDNA ITS, LEAFY, and GBSSI (two putative copies), along with morphological characters, recognize two clades (series Crataegifolia and Micrantha). However, chloroplast phylogenies based on ndhF, trnL-F, and psbA-trnH are significantly incongruent with the nuclear trees, showing two major clades with species from the Asian continent excluding the northeast (AS - N) in one clade and those from Asian Pacific Islands plus northeast Asia in the other (API N). Ancient hybridization and chloroplast capture may have occurred in the two series in both geographic areas. The two series diverged at 46.3 mya, which is before the formation of the Japanese Sea in the early Miocene (32–18 mya). The Japanese Sea may be the barrier for the seed exchange between the two geographic areas, and was responsible for the formation of the disjunct distribution of section Macrantha between the AS N and API N areas, and between eastern Asia and North America.