A phylogenetic analysis was carried out to clarify the systematic position of Gyrocheilos and Didymocarpus, particularly the species placed in Didymocarpus sect.Heteroboea by Wang et al. Based on sequencing the internal transcribed spacer and the chloroplast spacer trnL-F, parsimony and Bayesian inference analyses were carried out using separate nuclear and chloroplast datasets, as well as a combined dataset. Our results showed that the two sections of Didymocarpus in China andGyrocheilos did not form separate monophyletic subclades, but turned up in three different places in the phylogenetic trees. In the frame of the present study, the pollen morphology of the species included in the analysis was studied. It proved inconsistent with the delimitation between Didymocarpus and Gyrocheilos. Furthermore, pollen and other morphological characters indicate that Gyrocheilos and some taxa of Didymocarpus should be placed within Didymocarpus.