Acer is one of the most diverse woody genera in the Northern Hemisphere. Recent phylogenetic studies support the placement of Acer and Dipteronia—sole members of the traditional Aceraceae—in the Sapindaceae. However, the monophyly of Acer and its sections remain to be tested. In this study, sequences of two chloroplast non-coding regions, psbM-trnD and trnD-trnT, are used to elucidate phylogenetic relationships of Acer and Dipteronia. Our results support the monophyly of Acer and sects. Arguta, Ginnala, Integrifolia, Lithocarpa, Macrantha, Palmata, Platanoidea, and Trifoliata. In contrast, sects. Acer, Goniocarpa, Parviflora, Saccharodendron, and Spicata are not monophyletic. Acer trautvetteri and A. opalus of sect. Acer are more closely related to A. monspessulanum of sect. Goniocarpa and A. saccharum of sect. Saccharina than to A. caesium and A. pseudoplatanus of sect. Acer. Acer distylium of sect. Parviflora is more closely related to sect. Platanoidea than to A. nipponicum of sect. Parviflora. Morphological species pairs between eastern Asia and North America are not sister species, including A. pycnanthum—A. rubrum and A. caudatum—A. spicatum. Acer ukurunduense is a distinct species from A. caudatum. Acer glabrum is most closely related to A. pseudoplatanus, whereas A. spicatum may be more closely related to A. carpinifolium than to A. caudatum. Section Hyptiocarpa is most closely related to sect. Rubra, and the two North American species of sect. Rubra (A. rubrum and A. saccharinum) are more closely related to each other than they are to the Japanese species (A. pycnanthum). Sections Integrifolia and Trifoliata are closely related, and so are Cissifolia and Arguta. Nevertheless, more data are needed to fully resolve intersectional relationships of Acer.