Many species of large herbivores are declining in numbers as a consequence of direct exploitation or habitat loss. In the Ethiopian highlands, rapid human population growth has resulted in an expansion of human settlements and farmland, threatening many endemic species such as the mountain nyala Tragelaphus buxtoni. Despite being listed as an endangered species, the mountain nyala is still the most important trophy hunting species in Ethiopia. We counted faecal pellets of mountain nyala within plots distributed along transects to estimate population size and identify key environmental variables associated with the presence of faecal pellet groups. The total mountain nyala population was estimated at 3756 (95% confidence intervals: 2506–7135) individuals, mainly occupying woodlands while avoiding human developments (agriculture and settlements). The total suitable area was estimated at 8333 km2. Only 31.6% of the total population lived within a national park, while 53.5% of the population inhabited two controlled hunting areas in the eastern mountains. Abundance was 3.7 times higher in areas patrolled by wardens, regardless of being in a national park or hunting area, suggesting that formal protection must be followed by surveillance to avoid poaching and habitat destruction. We found no negative correlation between pellet abundance and trophy hunting. Yet, it is too early to conclude that trophy hunting is sustainable as it has only recently been initiated in the studied populations.