The monogeneric Daphniphyllaceae contain 36 taxa in the genus Daphniphyllum Blume that are endemic to Southeast Asia. Daphniphyllum is a morphologically homogeneous group of evergreen shrubs to trees divided into three sections: Daphniphyllum, Lunata T. C. Huang, and Staminodia Hurusawa. While the medicinal value of the Daphniphyllaceae has been explored in many studies, the understanding of their evolutionary history and infrageneric classification is still limited. To test the infrageneric classification and to examine evolutionary and classification hypotheses proposed by previous taxonomic studies, we reconstructed multilocus phylogenies by sampling 55.6% (= 20/36) of taxa in the genus based on both chloroplast (psbA-trnH spacer and trnL intron) and nuclear ITS (ITS1, 5.8S rDNA, and ITS2) regions. Our data do not support the monophyly of the three sections. Our results indicate that some hybridization events might have occurred in the evolutionary history of the genus. Moreover, our results support the classification hypotheses of D. glaucescens Blume in a strict sense but not in a broad sense. In addition, we elevate D. ×lanyuense (T. C. Huang) M. S. Tang, S. H. Liu & Yuen P. Yang, stat. nov., from varietal rank to species based on our results. Two putative natural hybrids, D. ×lanyuense and D. teijsmannii Zoll. ex Teijsm. & Binn., and their putative parental taxa are also revealed in our study. In sum, our results shed new insights into the sectional scope and understanding of evolutionary relationships among taxa in Daphniphyllum.