The Dzungarian Alatau in Central Asia and the Western Carpathians in Central Europe are exposed to anthropogenic sources of pollution that are impacting high-altitude mountain systems through long-range transport of emissions. Based on analyses of the autumn faeces of two species of marmots (Marmota baibacina from the alpine habitats of Zhongar Alatau National Park, Marmota marmota latirostris from the alpine habitats of the Western Tatras), we determined the environmental load of mercury and other chemical elements. Our results show significantly higher levels of total mercury amounts (p <
0.0001) in faeces of marmots from the Western Tatras, Slovakia (mean = 0.066 µg/g dry weight
SD = 0.43), than in Zhongar Alatau National Park, Kazakhstan (mean = 0.034 µg/g dry weight
SD = 0.01), as well as sulphur and heavy metals (Ba, Mn, Mo, Zn, Cu, and Cr) that originate from anthropogenic activities. Other significant differences in levels of mineral nutrients (K, Cl, Ca, Fe) and Sr rather indicate differences in food sources reflecting environmental factors.