The phylogeny of Brassaiopsis (Araliaceae), a morphologically diverse and widely distributed genus in Asia, was estimated based on sequences of the internal transcribed spacer regions (ITS) and 5S nontranscribed spacer (5S-NTS) of the nuclear ribosomal DNA. Two main paralogous copies of 5S-NTS were found for Brassaiopsis but both were not recovered for all species. All but one species of Brassaiopsis was represented by 5S-NTS (copy 1). Separate parsimony analyses of ITS and 5S-NTS (copy 1) generated largely congruent topologies, but several paralogous 5S-NTS sequences precluded data combination. A sister relationship of Brassaiopsis with Trevesia was strongly inferred. The divergence of Brassaiopsis from Trevesia was estimated to have occurred ca. 20 million years ago (MYA) during a period of mountain building and climatic change in SE Asia. Our analysis suggests a rapid evolutionary radiation of Brassaiopsis in the Sino-Himalayan region and Indochina at ca. 8 MYA. Several clades within the genus were circumscribed based on ITS and 5S-NTS analyses: 1) B. aculeata, B. glomerulata, and B. hainla; 2) B. gigantea, B. grushvitzkyi, B. moumingensis, and B. stellata; 3) B. ciliata and B. hispida; 4) B. fatsioides and B. palmipes; and 5) B. gracilis and B. phanerophlebia. Brassaiopsis producta is morphologically unique in possessing a 3–5-locular ovary, and its phylogenetic position was not well resolved in either analysis. Morphological characters previously considered important for defining species and subgeneric groups were shown to have had multiple origins (e.g., leaf architecture and locule number in the ovary). The Brassaiopsis phylogeny supports strong biogeographic connections between S China and Indochina, S China and SW China, and SW China and the eastern Himalayas.