Although the phylogenetic relationships of Apis species (Hymenoptera: Apidae) have been generally accepted, genetic variation within most species and some new possible species' status have not been studied in detail. In this study, we surveyed the genetic variation of mitochondrial DNA sequences in Apis species from China and investigated the phylogeography of Apis dorsata F. in China and neighboring Asian areas. The phylogeny of Chinese Apis species was consistent with the generally accepted Apis phylogeny, and a substructure within A. dorsata was suggested. Furthermore, results of analysis of molecular variance revealed significant genetic structuring of A. dorsata between Hainan Island and China mainland. When compared with neighboring Asian areas, Chinese A. dorsata grouped with one A. dorsata sample from Palawan Island of Philippines and two samples from Malaysia. Another two samples from Malaysia clustered with one Nepalese sample and the cluster from Thailand also was supported. These results support the hypothesis that glaciations and deglaciations during the Pleistocene could have greatly influenced the distribution and divergence of A. dorsata in China and Southeast Asia. In addition, the species status of Apis dorsata breviligula Maa and Apis dorsata binghami Cockerell were supported in our study and genetic variation may exist in Apis laboriosa Smith despite of limited natural distribution.