Aim The biogeography and speciation of conifers are of special interest because of the ecological importance of these trees, but the boundaries and evolutionary relationships of closely related species of conifers are difficult to disentangle. To investigate how lineage sorting and gene flow affect species boundaries in conifers, we studied the population genetic structure and phylogeo-graphical history of the Tsuga chinensis-T. forrestii complex and compared the results with those for a closely related species, T. dumosa. Location Subtropical eastern Asia. Methods Phylogeographical analyses, in combination with coalescent simulations, were performed based on sequence variation of paternal chloroplast and maternal mitochondrial DNA in 1368 individuals from 52 populations of the three Tsuga (hemlock) species. Results Mitotypes were shared extensively among the three species while the chlorotypes were relatively more species-specific. Two genetic breaks and thus three distinct geographical groups were identified in the T. chinensis-T. forrestii species pair. Unidirectional pollen flow from T. forrestii to T. chinensis was detected. Main conclusions Tsuga forrestii originated from a pre-existing isolate of T. chinensis, and a cryptic genetic break formed between eastern and western populations of the latter. Incomplete lineage sorting was responsible for the extensive sharing of mitotypes among the three hemlock species, and our results seem to support the idea that paternally inherited markers are more effective in delimiting species than maternally inherited markers. We also found that hemlock populations in the Himalayas were very likely to have experienced extinction, but that most populations in other areas of subtropical mainland China survived the late Quaternary glacial cycles by elevational shifts.