Populations of Balanophora from southern China are often identified by local botanists as B. laxiflora based on their long cylindric male inflorescence, subsessile male flowers with slender rudimentary bracts, and subdiscoid synandria. In this study, we clarify the identity of seven such populations based on morphological characters and phylogenetic analysis using nuclear 18S and ITS ribosomal DNA sequences. We confirmed the occurrence of dioecious populations of B. yakushimensis and two previously unrecognized species, which we describe here as B. parajaponica and B. appressa. Phylogenetic analyses indicated that B. parajaponica, B. yakushimensis, B. appressa, B. laxiflora, and the agamospermic B. japonica, formed a well resolved clade, viz. the B. laxiflora clade. The four dioecious species, although highly similar in the morphology of male inflorescence and flowers, can be separated by leaf morphology and arrangement, ovary color, and arrangement of female flowers. The species limit of B. laxiflora, however, remains unresolved.