The recently described genus Shaniodendron (Chang)Deng, Wei et Wang (Hamamelidoideae, Hamamelidaceae) is monotypic, narrowly distributed in eastern China, and on the verge of extinction. Morphological analysis puts this genus in the Fothergilleae sensu Harms, and implies that Shaniodendron is closely related to Parrotia C. A. Mey. In this study, sequences of the internal transcribed spacers of nuclear ribosomal DNA were analyzed for apetalous genera of the Hamamelidoideae to further evaluate the systematic relationships of Shaniodendron. The ITS-based phylogeny supported the combination of the Distylieae and the Fothergilleae, thus recognizing the Fothergilleae sensu Endress. It also substantiated the close relationship of Shaniodendron and Parrotia. The estimated divergence time of Shaniodendron and Parrotia was the late Miocene, which agreed with the fossil record.