To explore the biogeographical patterns of endophytic fungal communities on a large scale, we surveyed fungal endophytes in roots of Stipa krylovii from six vegetation types in grassland along a 3200 km west-east transect in northern China. Pyrosequencing of samples collected from 18 sites (three sites per vegetation type) revealed that Pleosporales, Hypocreales, Agaricales, and Xylariales were the dominant fungal orders in roots of S. krylovii. The dominant genera were Marasmius, Fusarium, Acremonium, Sarcinomyces, and Monosporascus, and these genera were distributed differently among the six vegetation types. In a variation partitioning analysis, vegetation type, geographical distance, and environmental parameters (mean annual precipitation and air temperature, soil organic carbon, soil total nitrogen, pH, elevation) explained 98.2% of variation in the endophyte fungal community, and environmental parameters explained more variation than did vegetation type or geographical distance. Mean annual precipitation was the major significant factor influencing endophytic fungal communities.