<p>Orangutans (Pongo spp.) are endangered, and rehabilitation programs have been conducted in many areas of Borneo and Sumatra. However, there is a general concern about the decline in genetic diversity in semi-wild populations that repeatedly breed in small numbers and with limited genetic exchange with external populations. In this study of Bornean orangutans in Sabah, Malaysia, non-invasive samples were collected from 28 individuals in a semi-wild population at the Sepilok Orangutan Rehabilitation Centre and 31 in a wild population at the Danum Valley Forest Reserve. Eleven microsatellite loci were used to evaluate the genetic characteristics of the two populations. Contrary to expectations, the number of alleles and heterozygosity were higher in the semi-wild population than in the wild population, indicating no trend toward reduced genetic diversity in the semi-wild population. One possible reason is that the semi-wild population includes individuals rescued from multiple remote areas. We then simulated sustainability with PVA (population viability analysis) to predict population size fluctuations over 1,000 years after accounting for differences in demographic factors, carrying capacity, and reproductive parameters of the two populations. The results indicated that the wild population had a relatively low risk of extinction. In contrast, the semi-wild population was predicted to be likely to become extinct after 200 years, due to the small initial population size and the lower environmental carrying capacity. This suggests that systematic management is necessary to maintain the population over the long term, depending on conditions.</p>