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Background  The evolutionary history of the Asian colobines is less understood. Although monophyly of the odd-nosed monkeys was recently confirmed, the relationships among the langur genera  Presbytis ,  Semnopithecus  and  Trachypithecus  and their position among Asian colobines remained unclear. Moreover, in  Trachypithecus  various species groups are recognized, but their affiliations are still disputed. To address these issues, mitochondrial and Y chromosomal sequence data were phylogenetically related and combined with presence/absence analyses of retroposon integrations.    Results  The analysed 5 kb fragment of the mitochondrial genome allows no resolution of the phylogenetic relationships among langur genera, but five retroposon integrations were detected which link  Trachypithecus  and  Semnopithecus . According to Y chromosomal data and a 573 bp fragment of the mitochondrial cytochrome b gene, a common origin of the species groups  T . [ cristatus ],  T . [ obscurus ] and  T . [ francoisi ] and their reciprocal monophyly is supported, which is also underpinned by an orthologous retroposon insertion.  T . [ vetulus ] clusters within  Semnopithecus , which is confirmed by two retroposon integrations. Moreover, this species group is paraphyletic, with  T. vetulus  forming a clade with the Sri Lankan, and  T. johnii  with the South Indian form of  S. entellus . Incongruence between gene trees was detected for  T . [ pileatus ], in that Y chromosomal data link it with  T . [ cristatus ],  T . [ obscurus ] and  T . [ francoisi ], whereas mitochondrial data affiliates it with the  Semnopithecus  clade.    Conclusion  Neither relationships among the three langur genera nor their position within Asian colobines can be settled with 5 kb mitochondrial sequence data, but retroposon integrations confirm at least a common origin of  Semnopithecus  and  Trachypithecus . According to Y chromosomal and 573 bp mitochondrial sequence data,  T . [ cristatus ],  T . [ obscurus ] and  T . [ francoisi ] represent true members of the genus  Trachypithecus , whereas  T . [ vetulus ] clusters within  Semnopithecus . Due to paraphyly of  T . [ vetulus ] and polyphyly of  Semnopithecus , a split of the genus into three species groups ( S. entellus  - North India,  S. entellus  - South India +  T. johnii ,  S. entellus  - Sri Lanka +  T. vetulus ) seems to be appropriate. T. [ pileatus ] posses an intermediate position between both genera, indicating that the species group might be the result of ancestral hybridization.

Phylogenetic position of the langur genera Semnopithecus and Trachypithecus among Asian colobines, and genus affiliations of their species groups