<p>Soil ecosystems are crucial for supporting life, yet little is known about their biodiversity and its distribution in extreme environments. The Atacama Desert, the driest non-polar desert on Earth, has scarce water, high salinity, and metal-rich water bodies, creating challenging conditions for most organisms. Above-ground life has been partially documented, but its soils remain poorly studied. Here we show that soil nematodes, an abundant and diverse group of invertebrates, display distinct biodiversity patterns across the Atacama at multiple biological scales, including genetic, taxonomic, community, and life-cycle levels. Surveys across dune systems, high-altitude mountains, saline lakes, river valleys, and fog oases reveal unique assemblages in each habitat. We find that asexual taxa are more common at higher altitudes, consistent with patterns of geographical parthenogenesis. Genus richness follows a latitudinal gradient and increases with precipitation. These results demonstrate that even in one of the most extreme terrestrial environments, stable soil communities can persist. However, evidence of simplified soil food webs suggests vulnerability to further environmental change. Our findings provide new insights into the mechanisms shaping biodiversity in arid ecosystems and can inform predictions about soil resilience under global climate-driven aridification.</p>