We sought to test the utility of two single-copy nuclear genes for resolving phylogenetic relationships within the woody plant tribe, Acereae (Sapindaceae). Acereae comprises Acer (125 spp.) and Dipteronia (2 spp.), two genera that possess schizocarpic fruits, which split into two winged mericarps. In Acer, the mericarps are elongated with a basally arranged locule and a dorsal or distal wing. In Dipteronia, the mericarp is obovate, and the locule is located centrally and surrounded by the wing. We analyzed 35 species of Acer representing 12 of 16 taxonomic sections plus Dipteronia sinensis to elucidate the phylogeny of Acereae using the single-copy nuclear genes AT103 and SQD1. Both genes exhibited limited variation in Acereae and, therefore, provided limited support for phylogenetic relationships. The phylogeny of concatenated AT103 and SQD1 showed Dipteronia sinensis within Acer with negligible support (0.14 posterior probability, < 50% maximum parsimony bootstrap, MP-BS), a position that is congruent with results from prior studies using chloroplast DNA and internal transcribed spacer (ITS). Based on our results and results from prior studies, we discuss implications for leaf and fruit evolution in Acereae.