Balanophora subgen. Balania (Balanophoraceae), whose members differ from those of the other subgenus in having three-merous male flowers, includes B. flava, B. involucrata, B. tobiracola, the B. harlandii assemblage, and the agamospermic species B. japonica. Species limits of B. flava, B. involucrata, and the B. harlandii as currently circumscribed (B. harlandii assemblage) have long been controversial. Here, species limits in subgen. Balania are explored based on morphological characters and phylogenetic analysis using nuclear 18S and ITS ribosomal DNA sequences. Subgen. Balania was monophyletic if B. japonica is excluded. Balanophora harlandii assamblage was polyphyletic and three lineages, B. harlandii, B. kawakamii, and B. henryi, were recovered in the assemblage. Molecular and morphological divergence, distribution, and phenology provided strong support for the recognition of these lineages as distinct species, namely B. harlandii, B. kawakamii, and B. henryi. The findings also suggested that B. flava should be reduced to synonym under B. involucrata, thus supporting Hansen's treatment of both dioecious and monoecious populations as members of a single species.