The Kashmir musk deer (Moschus cupreus) is a globally endangered species hunted for its musk pod. Despite its endangered status, it remains one of the least studied species of musk deer. In 2019, the genetic discovery of Kashmir musk deer in Mustang district of Nepal – outside of its historically known range in Kashmir, India – opened up new avenues for research on this elusive species. Communication among individuals of musk deer is primarily based on latrine sites, which serve various purposes such as territorial marking and reproductive signaling. Hence, this study aims to investigate the association between microhabitat and latrine sites of Kashmir musk deer in the Mustang, Nepal. A systematic survey was conducted to identify latrine presence and absence sites at an elevational gradient. Data on biophysical parameters, including altitude, slope, aspect, tree height, shrub height, and regeneration height were recorded for both latrine presence and absence plots. Significant differences in tree height and regeneration height, crown cover, and trail width were observed between the presence and absence plots. Latrine presence and absence data fitted with the generalized linear model using logistic function, revealed that the interaction between tree height and regeneration height plays a pivotal role in determining the suitability of a particular site within the habitat for establishing a latrine site. This significant positive interaction indicated that the probability of discovering latrines significantly increases when the areas have taller trees and taller regeneration. This finding affects microclimate factors, such as sunlight exposure, wind speed, soil moisture, and temperature, influencing their role in sustaining scent retention in the latrine sites. Incorporating knowledge about the association between microhabitats and latrine sites can aid in preserving suitable habitats that are critical for establishing communication among individual musk deer. This information can inform various conservation efforts, including captive breeding programs, anti-poaching operations, and reintroduction initiatives.