Habitat loss and fragmentation, the illegal wildlife trade and exploitation for Traditional Chinese Medicine (TCM) threaten the sun bear (Helarctos malayanus) with extinction. The confiscation or rescue of bears affected by each of these threats results in an ethical dilemma for conservation practitioners as they must decide over the fate of the confiscated bear and which decision is in the interest of long-term species survival. To understand the conservation status of any species, it is essential to have access to as much long-term information as possible. This requires a standardized approach to communicate research results and approaches in order to inform scientists without the risk of data being miss-interpreted. Using the standardized PRISMA-p model (commonly applied in medical professions) in the systematic review of white literature on sun bears (Chapter 2) resulted in the Helarctos-database that will be made publicly available. This method allowed for a standardized reporting on the current literature and revealed that the sun bear has been neglected by the scientific community. Furthermore, it identified genetic (and genomic) research on the sun bear as one of the main research gaps. Genetics and genomics find many applications in ex-situ and in-situ conservation. To protect species, it is essential to understand their evolutionary history and adaptation potential to a changing environment. In Chapter 3 of this thesis, the mitochondrial genomes of museum-derived, as well as contemporary, sun bear samples covering most of the distribution range of the sun bear were sequenced using next-generation sequencing methods. While phylogeography helps to resolve taxonomic uncertainties, identify species and sub-species that may be warranted conservation priority, it also allows the identification of geographical barriers that may have led to speciation events. This first phylogeographic study of the sun bear revealed that there are two lineages: the ‘mainland’ lineage and the ‘sunda’ lineage. These lineages were disconnected at the Isthmus of Kra (Thailand), due to seawater level rises during the Pleistocene. This study demonstrated that waterbodies, if large enough, can create a geographical barrier for sun bears. Understanding barriers to gene-flow is essential for the effective protection of a species. As the human landscape alteration is causing the fragmentation of habitats, understanding the population structure, gene-flow between populations and their genetic variability is becoming essential for conservation management. Chapter 4 of this thesis demonstrates for sun bears in Cambodia how microsatellite (nuclear) markers can identify the number of populations and how these populations are connected. Microsatellite markers are a useful tool to identify hybridization and inbreeding in populations and are therefore capable of identifying populations of conservation concern. This research revealed that there are two sun bear populations, East and West of the Mekong river in Cambodia, and that these two populations are exchanging genes (as is an admixed population). In the population in West Cambodia, inbreeding was detected, indicating that the current exchange of genes between the two populations is not sufficient to maintain genetic diversity in the West population. Currently it is not known what may have caused the loss of genetic diversity of the Western population but illegal wildlife trade may be implicated. Microsatellite markers could be used to develop forensic markers to combat the illegal wildlife trade and to identify endangered animals in TCM products. Although the sun bear is used in TCM products, it is not understood to what level the TCM industry is threatening the sun bear. The fifth Chapter of the thesis tested forensic DNA extraction protocols, extraction kits and Gas-Chromatography Mass Spectrometry (GC-MS) on different Traditional Chinese Medicine products, to determine whether these samples contain sun bear derivate. Currently there are many forensic methods with reference databases for the Asiatic black bear but none regarding the sun bear. The forensic genetic methods employed here were not successful in heavily processed TCM products as they likely did not appear to contain any intact DNA. Therefore, the further development of genetic and non-genetic forensic method to detect sun bear is required. The final Chapter discusses how the findings of the previous Chapters can inform sun bear conservation practitioners who must decide whether they release a sun bear or whether they maintain it in captivity and advises on direct conservation action. Releasing a bear requires detailed knowledge and access to this knowledge about the species. The Helarctos-database would provide a one-stop for sun bear research. The phylogeography analysis identified that two genetically distinct lineages of sun bears. Although the study did not obtain enough samples to conclude on species and subspecies classification, understanding that the sun bears on the mainland are different to the sun bears on the Sunda islands is important for ex-situ breeding and release efforts. The microsatellite study demonstrated that nuclear markers can identify population hybridization, geographical barrier and inbreeding. In the West Cambodian sun bear population inbreeding was detected. This informs conservation actions such as potential augmentation, establishment of connectivity and further research. This study also successfully assigned sun bears of unknown origin to a potential source population, which is critical information for release projects. Furthermore, the forensic analysis of TCM products of sun bears highlighted that forensic methods currently available are ineffective on heavily processed TCM samples and need to be further developed. Being able to test whether sun bear derivate is present in TCM products is necessary to judge the level of threat imposed by the TCM industry on the Malayan sun bear.