Despite the widespread occurrence of fungal endophytes (FE) in plants inhabiting arid ecosystems, the environmental and soil factors that modulate changes in FE diversity and community composition along an aridity gradient have been little explored. We studied three locations along the coast of the Atacama Desert in Chile, in which the plant Aristolochia chilensis naturally grows, and that differ in their aridity gradient from hyper-arid to semi-arid. We evaluated if root-associated FE diversity (frequency, richness and diversity indexes) and community composition vary as a function of aridity. Additionally, we assessed whether edaphic factors co-varying with aridity (soil water potential, soil moisture, pH and nutrients) may structure FE communities. We expected that FE diversity would gradually increase towards the aridity gradient declines, and that those locations that had the most contrasting environments would show more dissimilar FE communities. We found that richness indexes were inversely related to aridity, although this pattern was only partially observed for FE frequency and diversity. FE community composition was dissimilar among contrasting locations, and soil water availability significantly influenced FE community composition across the gradient. The results indicate that FE diversity and community composition associated with A. chilensis relate to differences in the aridity level across the gradient. Overall, our findings reveal the importance of climate-related factors in shaping changes in diversity, structure and distribution of FE in desert ecosystems.