Premise of the research. The disjunct distribution of plant genera between eastern Asia (EA) and eastern North America (ENA) has long attracted the attention of biologists and biogeographers. For most genera that have been studied, there are more species in EA than ENA and the diversity anomaly may have resulted from the greater physiographical heterogeneity in conjunction with climate and sea level changes in EA than in ENA. However, few empirical studies have explicitly tested the association between species diversity and allopatric speciation events. The genus Stewartia (Theaceae) displays this diversity anomaly with two species in ENA and 21 species in EA, but the phylogeny of this group has not been resolved due to insufficient data. Methodology. Here, we sampled 15 species of Stewartia (65%) and generated data from over 500 nuclear loci using the anchored phylogenomic approach to produce a robust phylogeny of Stewartia. In addition, biogeographical analyses were performed to elucidate the natural history of Stewartia including estimated times of divergence, ancestral areas, and speciation patterns. Pivotal results. Our parsimony, Bayesian, and species tree analyses produced congruent phylogenies with high resolution of the interspecific relationships within Stewartia. Speciation in Asia was mostly allopatric between the Japanese islands and the Asian continent during the Miocene and early Pliocene, while the two ENA species represent lineages from different times with S. malacodendron being the first lineage to split off from the remaining species and S. ovata coming later sister to the deciduous species of Asian Stewartia. Conclusions. The results provide direct evidence for the importance of allopatry in the differential diversity between EA and ENA.