Orangutans are only found in Northern Sumatra (Pongo abelii), West and East Kalimantan, Sarawak and Sabah on Borneo (Pongo pygmaeus). Fragmentation and deforestation of lowland tropical forests in those areas have changed the habitats and forced the orangutans into small populations. These small populations threaten the existence of the species. For this reason, definition of appropriate conservation units is required in order to save the orangutans from extinction. The recent studies about Sumatran orangutan populations show a high difference in the genetic population structure between north of Toba and south of Toba. This is influenced by the eruption of the Toba volcano around 1.2 mya. Mitochondrial DNA analysis shows that populations in Batang Toru are closer to the Bornean (2.26 mya) than other Sumatran orangutan populations (3.89 mya). My PhD study will be divided into two parts. The first aim of the study is to sample and analyze genetic data from six new locations. The second aim of my project study will be a more in-depth analysis of orang-utans south of Batang Toru area, a population that has been found to be genetically closer to Bornean orang-utans for some genetic markers. The second part of the study will be carried out using historical museum samples (samples origins: Padang Cave and Fort the Kock, West Sumatra). I intend to utilise mitochondrial DNA, Y- chromosome, and microsatellite markers to analyze the genetic population structure. The result of this study will complete the Sumatran orangutan’s genetic database and generate the appropriate conservation units for Sumatran orangutan’s conservation.