Gibbons of the genus Hylobates likely speciated very rapidly following isolation by rising sea levels during the Pleistocene. We sequenced the hypervariable region I (HV-I) of the mitochondrial D-loop to reconstruct the phylogeny of this group. Although the results clearly supported monophyly of each of the six species, the relationships among them were not clearly resolved by these data alone. A homogeneity test against published data sets of a coding mitochondrial locus (ND3-ND4 region), behavioral characters (vocalizations), and morphological traits (including skeletal and soft tissue anatomy) revealed no significant incongruence, and combining them resulted in a phylogenetic tree with much stronger support. The Kloss's gibbon (H. klossii), long considered a primitive taxon based on morphology, shares many molecular and vocal characteristics with the Javan gibbon (H. moloch), and appear as the most recently derived species. The northernmost species (H. lar and H. pileatus) are the most basal taxa. These data suggest that ancestral gibbons radiated from north to south. Unlike other markers, the HV-I region can accurately identify members of different gibbon species much like a DNA barcode, with potential applications to conservation.