Understanding how fungal endophyte communities differ in abundance, diversity, taxonomic composition, and host affinity over the geographic ranges of their hosts is key to understanding the ecology and evolutionary context of endophyte-plant associations. We examined endophytes associated with healthy photosynthetic tissues of three closely related tree species in the Cupressaceae (Coniferales): two native species within their natural ranges [Juniperus virginiana in a mesic semideciduous forest, North Carolina (NC); Cupressus arizonica, under xeric conditions, Arizona (AZ)], and a non-native species planted in each site (Platycladus orientalis). Endophytes were recovered from 229 of 960 tissue segments and represented at least 35 species of Ascomycota. Isolation frequency was more than threefold greater for plants in NC than in AZ, and was 2.5 (AZ) to four (NC) times greater for non-native Platycladus than for Cupressus or Juniperus. Analyses of ITS rDNA for 109 representative isolates showed that endophyte diversity was more than twofold greater in NC than in AZ, and that endophytes recovered in AZ were more likely to be host-generalists relative to those in NC. Different endophyte genera dominated the assemblages of each host species/locality combination, but in both localities, Platycladus harboured less diverse and more cosmopolitan endophytes than did either native host. Parsimony and Bayesian analyses for four classes of Ascomycota (Dothideomycetes, Sordariomycetes, Pezizomycetes, Eurotiomycetes) based on LSU rDNA data (ca 1.2 kb) showed that well-supported clades of endophytes frequently contained representatives of a single locality or host species, underscoring the importance of both geography and host identity in shaping a given plant's endophyte community. Together, our data show that not only do the abundance, diversity, and taxonomic composition of endophyte communities differ as a function of host identity and locality, but that host affinities of those communities are variable as well.