The origin and population history of the endangered golden snub-nosed monkey (Rhinopitheucs roxellana) remain largely unavailable and/or controversial. We here integrate analyses of multiple genomic markers including mitochondrial (mt) genomes, Y chromosomes and autosomes of 54 golden monkey individuals from all three geographic populations (SG, QL and SNJ). Our results reveal contrasting population structures. Mt analyses suggest a division of golden monkeys into five lineages, one in SNJ and two in SG and two in QL. One of the SG lineages (a mixed SG/QL lineage) is basal to all other lineages. In contrast, autosomal analyses place SNJ as the most basal lineage and identify one QL and three SG lineages. Notably, Y analyses bears features similar to mt analyses in placing the SG/QL-mixed lineage as the first-diverging lineage and dividing SG into two lineages, while resembles autosomal analyses in identifying one QL lineage. We further find bi-directional gene flow among all three populations at autosomal loci, while asymmetric gene flow is suggested at mt genomes and Y chromosomes. We propose that different population structures and gene flow scenarios are the result of sex-linked differences in the dispersal pattern of R. roxellana. Moreover, our demographic simulation analyses support an origin hypothesis suggesting that the ancestral R. roxellana population was once widespread and then divided into SNJ and non-SNJ (SG and QL) populations. This differs from previous mt-based "mono-origin (SG is the source population)" and "multi-origin (SG is a fusion of QL and SNJ)" hypotheses. We provide a detailed and refined scenario for the origin and population history of this endangered primate species, which has a broader significance of Chinese biogeography. In addition, this study highlights the importance to investigate multiple genomic markers with different modes of inheritance to trace the complete evolutionary history of a species especially for those exhibiting differential or mixed patterns of sex dispersal