Genetic diversity is the raw material for species' persistence over time, providing the potential to survive stochastic events, as well as climate and/or human-induced environmental changes. Biodiversity in dry rangelands is decreasing due to intensification of livestock production, but its effects on the genetic diversity of the consumed biota have seldom been assessed. We examined livestock effects on the genetic diversity of two dominant creosote species of the Patagonian Monte Desert, Larrea divaricata and Larrea cuneifolia. We deployed competing hierarchical regression models to assess the relationship between genetic variation within natural populations as a function of increasing stocking rates on ten arid rangelands. These species exhibit similar levels and patterns of genetic structure, with high levels of both inbreeding and divergence among locations. We found that increased stocking reduces genetic variation and increases genetic subdivision between populations. Our results indicate that grazing pressures are impoverishing the gene pool of these dominant native species of the Monte Desert, decreasing the evolutionary potential of the primary plant producers and increasing the desertification risk for a vulnerable habitat. We highlight the importance of considering livestock as a major driver of genetic losses in dry rangelands under overgrazing pressure, especially given current forecasts of climate change.