We investigated the levels of natural resource use by humans and the consequent response of wild mountain ungulates in the subalpine and alpine habitats of Bedini-Ali, located in the transition zone of the Nanda Devi Biosphere Reserve, India, from 2005 to 2006. The livestock population in the area, livestock dung density, and the number of trees cut, lopped, and debarked by humans were estimated from permanent plots (n = 312, 8 visits) laid along transects. Information on wild mountain ungulate distribution, abundance, and habitat use was recorded by monitoring transects (n = 7, 1.2–2 km, 217 visits, 325.5 km sampled) and scanning (n = 2, 10 replicates, 60 hours effort). Principal coordinates of overall disturbance were classified into 3 classes: low (< −0.04), moderate (≥ −0.04 to <0), and high (≥ 0). Blue sheep (Pseudois nayaur) was most commonly encountered [46 sightings, 652 individuals, 10.19 ± 1.20 (number/hour scan)] in the alpine regions, followed by sambar (Cervus unicolor) (15 sightings, 18 individuals, 0.65 ± 0.01/km) and Himalayan musk deer (Moschus chrysogaster) (3 sightings, 3 individuals, 0.0015 ± 0.001/km) in subalpine areas. Abundance estimates for all wild ungulates were lowest during summer when anthropogenic activities were highest. Density of blue sheep and dung density of sambar and musk deer varied seasonally and was inversely related to livestock abundance. Blue sheep were spatially separated from other ungulates on high-altitude steep rocky terrain with low anthropogenic pressure. Sambar and musk deer had to share the subalpine and tree line forested habitats with herded livestock. Prior utilization of food resources in summer by livestock and habitat destruction due to other anthropogenic pressures may have negative impacts on the population of wild mountain ungulates in the study area. We recommend adoption of rotational grazing between Bedini and Ali Meadows, reduction in the number of livestock, and reduction in the period of grazing as mitigation measures.