Species delimitation is fundamental to conservation and sustainable use of economically important forest tree species. However, the delimitation of two highly valued gold-thread nanmu species (Phoebe bournei (Hemsl.) Yang and P. zhennan S. K. Lee & F. N. Wei) has been confusing and debated. To address this problem, we integrated morphology and restriction site-associated DNA sequencing (RAD-seq) to define their species boundaries. We obtained consistent results from the two datasets, supporting two distinct lineages corresponding to P. bournei and P. zhennan. In P. bournei, higher order leaf venation is more prominent, petioles are thicker, and leaf apex angle is narrower, compared to P. zhennan. Both datasets also revealed that the former putative P. bournei populations from northeastern Guizhou belong to P. zhennan. The two species are now distinct in distributions except in the Wuling Mountains, where they overlap. Phoebe bournei occurs mainly in central Fujian, southern Jiangxi, the Nanling Mountains, and the Wuling Mountains, whereas P. zhennan is found in the adjoining eastern regions of the Qionglai Mountains, the southern Sichuan hills, and the Wuling Mountains. The re-delimitation of P. bournei and P. zhennan and clarification of their ranges provide a better scientific basis guiding the conservation and sustainable utilization of these tree species.