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[Display omitted] • The autosome, mitogenome, and Y-chromosome analyses revealed three monophyletic clades for M. fuscata , M. cyclopis , and M. mulatta. • The disparate demographic trajectories revealed that M. cyclopis and M. fuscata derived from the ancestral M. mulatta population. • The divergence time between M. cyclopis and M. fuscata occurred at the beginning of the "Ryukyu Coral Sea Stage" (1.0-0.2 Ma). • The three parallel rivers (Nujiang, Lancangjiang, and Jinshajiang) divided M. mulatta into Indian and Chinese genetic populations ∼200 kya. Climate changes at larger scales have influenced dispersal and range shifts of many taxa in East Asia. The fascicularis species group of macaques is composed of four species and is widely distributed in Southeast and East Asia. However, its phylogeography and demographic histories are currently poorly understood. Herein, we assembled autosomal, mitogenome, and Y-chromosome data for 106 individuals, and combined them with 174 mtDNA dloop haplotypes of this species group, with particular focus on the demographic histories and dispersal routes of Macaca fuscata , M. cyclopis , and M. mulatta. The results showed: (1) three monophyletic clades for M. fuscata , M. cyclopis , and M. mulatta based on the multiple genomics analyses; (2) the disparate demographic trajectories of the three species after their split ∼1.0 Ma revealed that M. cyclopis and M. fuscata were derived from an ancestral M. mulatta population; (3) the speciation time of M. cyclopis was later than that of M. fuscata , and their divergence time occurred at the beginning of "Ryukyu Coral Sea Stage" (1.0–0.2 Ma) when the East China Sea land bridge was completely submerged by the sea level rose; and (4) the three parallel rivers (Nujiang, Lancangjiang, and Jinshajiang) of Southwestern China divided M. mulatta into Indian and Chinese genetic populations ∼200 kya. These results shed light on understanding not only the evolutionary history of the fascicularis species group but also the formation mechanism of faunal diversity in East Asia during the Pleistocene. [ABSTRACT FROM AUTHOR]