Conservation monitoring is paramount for the gathering of information on species and populations in need of conservation actions. However, monitoring of the mountain bongo Tragelaphus eurycerus isaaci, a Critically Endangered antelope endemic to Kenya, has hitherto been limited to surveillance (i.e. focused on persistence of the species in particular areas), thus limiting the information that could be retrieved on the status and trends of these populations. Using a newly developed identification system, we implemented robust design mark–recapture using existing camera-trap records of four wild subpopulations of the bongo. We provide data on sex and age structure and the first estimates of population size in the wild. Males and calves seem to be suffering higher mortality than females, and only two of the four monitored populations include adults of both sexes and calves. The combined size of these two breeding populations is estimated to be 29–50. Our findings confirm the critical situation of the mountain bongo in the wild and highlight the need for conservation actions to reinforce the wild populations for the long-term conservation of this antelope.