Apterosperma and Euryodendron, monotypic genera in Theaceae (sensu lato), are endemic and restrictedly distributed in south China. The two genera are not included in the major classification systems. However, their systematic position and origin have been subject to intense debate in the last decade. In this study, the phylogeny and divergence times of both Apterosperma and Euryodendron were inferred using combined dataset of chloroplast DNA trnL-F and atpB-rbcL non-coding sequences and nrDNA ITS sequences. The results from Bayesian inference, maximum parsimony, and maximum likelihood consistently showed that (i) Euryodendron is a valid genus, which is closer to Eurya than to Cleyera and (ii) Apterosperma is a genus of the tribe Theeae along with Tutcheria and Camellia. It was first reported that the divergence time of Apterosperma was 61.98 million years ago (mya), whereas that of Euryodendron 20.51 mya, indicating Tertiary origins in south China. The divergence of Apterosperma appears to be the result of increased ecological opportunity after Cretaceous/Tertiary extinction events and related with high temperatures and high humidity environments. By contrast, the origin of Euryodendron may be associated with historical mountain building events as well as the significant climate changes that established cooler temperatures prevailing until today.