Endophytic fungi play a crucial role in plant health, contributing to stress tolerance, disease resistance, and ecological adaptation. However, the diversity and richness of endophytic fungal communities associated with Capparis spinosa L. in the Alborz, Tehran, and Qom provinces-ranging from semi-arid and slightly temperate to arid and desert climatic conditions-have not yet been investigated. Using morphological and molecular methods, we identified a diverse fungal assemblage comprising 3 phyla, 7 classes, 14 orders, 28 families, and 36 genera. Among the genera shared across all three provinces, Alternaria (28.8%) was the most dominant among the isolates, whereas Simplicillium (1.6%) was the least abundant. Analysis of the isolates using diversity indices revealed that species distribution in all three provinces tended toward evenness, with a similar pattern observed across different tissues. Qom exhibited the highest diversity and richness of fungal species. Additionally, a detailed comparison of different plant tissues revealed that roots consistently harbored the greatest variety and the highest number of isolates compared to stems, leaves, and fruits. Diversity metrics suggest a potential link between climatic gradients and endophyte diversity. These findings enhance our understanding of fungal-plant interactions and provide insights into the microbial contributions to C. spinosa resilience in harsh environmental conditions.