The vicuña (Vicugna vicugna) is a wild camelid native from South America, known for its highly valued fiber. In Bolivia, the Apolobamba protected area is a key area for vicuña conservation and Apolobamba’s indigenous communities sustainably harvest the fiber of wild vicuña. The vicuña is an important cultural and economic resource, as well as an indicator of ecosystem health. Over the last decade gold mining activities have increased in Apolobamba potentially causing high levels of mercury contamination, endangering the health of vicuñas, humans, and terrestrial ecosystems. This study used genotoxicity markers: micronuclei (MN) and nuclear abnormalities (NA) in buccal cells and lymphocytes of vicuñas in 13 vicuña management communities in Apolobamba. A mean frequency of 0.48% MN and 14.91% NA was found in buccal cells, and 0.32% MN and 57.13% NA in lymphocytes. A higher frequency of MN in buccal cells was expected as they are the first barrier to inhalation or ingestion of genotoxic agents. However, a higher frequency of NA in lymphocytes suggests a possible prevalence of damage. Furthermore, a gradient of MN frequency was observed consistently with mining activity, but mining may not be the only cause of this damage, as vicuñas are exposed to mixtures of environmental chemicals, including traces of microplastics and persistent organic pollutants that have been detected in the area too. These findings provide a baseline for future vicuña populations monitoring and can be used as bio monitors and sentinels of environmental pollution.