Endophytic plant-microbe interactions, universal across the land plants, range from mutualistic relationships that confer important ecological and agricultural traits to neutral or quasi-parasitic relationships. In contrast to substantial research on root and rhizosphere endophyte interactions, the role of environmental and host-related factors responsible for acquiring leaf endophyte communities remains relatively unexplored. In our research, we explore a novel approach using broad geographic coverage of North America within the restricted phylogenetic scope of the genus, Heuchera (Saxifragaceae), a recent plant host radiation. Heuchera has well-characterized phylogenetic relationships and diverse habitat specializations. We used strong host species and population sampling to assess microbial diversity at multiple host evolutionary levels, from phylogenetic to within-population diversity. Here we assess leaf endophyte diversity to test the hypothesis that membership of these microbial communities is driven primarily by abiotic environment and host phylogeny. Bacterial and fungal communities were characterized with 16S and ITS amplicon sequencing, using QIIME2 to call OTUs (operational taxonomic units) and calculate standard diversity metrics (species richness, Shannon diversity, phylogenetic diversity). We assembled a series of environmental predictors for bacterial and fungal diversity at collection sites including latitude, elevation, temperature, precipitation, and soil parameters. To account for spatial autocorrelation, a geographic distance matrix among sites was also calculated. Surprisingly, we find differing assembly patterns for bacterial and fungal endophytes. Using UniFrac distances to investigate community composition, we found that only host phylogeny is significantly associated with bacterial endophytes, while geography alone was the best predictor of fungal community composition. Species richness and phylogenetic diversity are very similar across sites and species, with only fungi showing a response to aridity and precipitation for some metrics. Unlike what has been observed with rhizosphere and root endophyte communities, in this system microbes show no relationship with pH or other soil factors. Our results indicate the importance of detailed clade-based investigation of microbiomes and the complexity of microbiome assembly within specific plant organs.