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The macaques, genus Macaca, represent one of the most successful primate radiations.With such a variety of range and species that differ in ecology and external morphology, macaques are considered as an alluring material to study the species radiation and evolution.It is critical to build a clear and accurate phylogeny of the macaques, which will contribute understand evolutionary history of the genus as well as primate radiations.The phylogenetic relationships among macaque species remain to be unclear and ambiguous solely based on morphology and mitochondrial DNA sequences.Incongruent phylogenetic relationships could be explained by incomplete lineage sorting, insufficient data, homoplasy, or hybridization in macaques.Combining a large number of genetic markers will benefit to imply the robust evolutionary history of macaque monkeys.In this study, phylogenetic relationships among eight macaques representing four species groups sylvanus, silenus, sinica and fascicularis and the outgroup taxon, Papio hamadray were investigated by a combining analysis based on the mitochondrial DNA, nuclear genes (including autosomal loci, fragments from Y chromosome and X chromosome) and presence/absence polymorphism of Alu elements.In the present study, we attempt to elucidate evolutionary relationships of the macaques and possible gene flows between species or groups.