The evolutionary processes driving patterns of genetic diversity and differentiation, and ultimately leading to speciation, are poorly understood. The aim of this thesis was to investigate the effects of environmental and biological mechanisms on gene flow and genetic diversity in the Bornean orang-utans, Specifically, I examined the effects of the Pleistocene climatic changes and riverine barriers as well as sex-biased dispersal. My results suggest that current Bornean orang-utan populations are the result of a recent radiation throughout the island, following the probable confinement within a glacial refugium in the Pleistocene. Furthermore, I found evidence for an extreme pattern of female philopatry and male-biased dispersal. These processes have led to highly structured genetic diversity, rendering the orangutans particularly vulnerable to anthropogenic effects and future climatic changes.