Abstract We carried out molecular phylogenetic analyses to examine the phylogenetic relationship of Ficus section Ficus (Moraceae) based on 22 species, 73 samples of the section, and 37 species, 41 samples representing other sections of Ficus. Four DNA sequences from the nuclear ribosomal internal transcribed spacer and the plastid trnH-psbA, psbK-psbI, and atpF-atpH intergenetic regions were selected. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian methods revealed that section Ficus was not monophyletic unless subsection Ficus was removed and that subsection Frutescentiae was monophyletic when excluding species such as F. tikoua Bureau, F. pedunculosa Miq., and F. neriifolia Sm. Ficus tikoua should be transferred from subgenus Ficus to subgenus Sycomorus. Ficus tuphapensis Drake should be transferred into subsection Frutescentiae from section Eriosycea. Our results also supported the placement of F. henryi Warb. ex Diels and F. subincisa Buch.-Ham. ex Sm. in subgenus Sycidium.