To assess the relatedness and amount of genetic variation of wild and captive Mountain Bongo Tragelaphus eurycerus ssp. isaaci, both non-invasive and invasive samples were efficiently analyzed using SNP’s. Mountain Bongo is estimated to remain in Kenyan forest with less than 96 individuals, possibly as low as 73 individuals, split in five subpopulations whereof four populations are isolated from each other. The genetic diversity of wild animals was studied using fecal samples, and using tissue samples from the 62 animals presently held captive at the Mount Kenya Wildlife Conservancy. In strategic conservation of the wild Mountain Bongo, the captive animals constitute a potential genetic input to wild populations. Our study shows there is still genetic variation in the wild population and that the subpopulations are to some extent genetically differentiated. This leads to an overall effective population size of around 14 in the wild population, which is good relative to the small population, but dangerously small for long-term, or even short-term, survival. Most individuals in the wild population were unrelated, while in the captive population most individuals were related at the level of half-sibs. The captive population still host genetic variation and is differentiated slightly to the wild population. Careful restocking from the captive populations could be an effective means to enhance the genetic variation in the wild, but most importantly make the dwindling population less vulnerable to stochastic events.