Despite several morphological and molecular analyses of Theaceae, several outstanding issues remain in the phylogenetics and biogeography of the family including the disputed relationships among the tribes Gordonieae, Stewartieae, and Theeae, the controversial taxonomic status of Hartia and Stewartia, and the unclear biogeographic history of Gordonieae and Stewartieae. In this study we gathered DNA sequences of multiple plastid genes from 27 species of Theaceae representing all genera except Laplacea, conducted phylogenetic analyses using parsimony, likelihood, and Bayesian methods, and estimated divergence times within a Bayesian framework with fossil calibrations and molecular data. Our data provided further support for the three tribes in the family and for the sister-group relationship of Theeae to Stewartieae plus Gordonieae. Within Gordonieae, our study for the first time offered strong molecular support for the sister relationship of Franklinia and Schima. Within Stewartieae, our data supported the paraphyly of Stewartia including Hartia. Within Stewartia, our data for the first time suggested that North American (NA) species Stewartia ovata was more closely related to eastern Asian (EA) species than to the other NA species Stewartia malacodendron. Biogeographic analyses indicated that disjunct endemic species of Gordonieae might have originated from NA and those of Stewartieae from EA. Divergence times of the EA-NA disjunct pairs identified in this study (Franklinia and Schima in Gordonieae and S. ovata (NA) and Asian species of Stewartia) were estimated to be in the Mid-Miocene. Population exchanges in Gordonieae and Stewartieae may have occurred over the Bering land bridge prior to the Mid-Miocene.