The well-known eastern Asia (EA) and eastern North America (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or clades isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these disjunct lineages. In this study, we compared foliar endophytes (including both fungi and bacteria) in 17 EA-ENA disjunct species pairs from genera representing conifers and major clades of angiosperms, as well as 23 species of Cornus from the US and China. We sequenced the ITS of fungi and 16S rDNA of bacteria to understand the composition of the endophyte community and gain insights into the relative roles of geographic isolation, host identity, phylogeny, and environment in shaping endophytic diversity patterns. We detected a much richer fungal than bacterial community in leaves of all species. Beta diversity varied greatly among individuals within species, between species, among genera, and among three natural environmental conditions. Based on a principal coordinates analysis, we found no close clustering of endophyte communities in samples from the same host plant species, from the same genus, or from the same geographic origin (i.e. EA or ENA) (when plants were grown in the same common garden), but we did detect clustering of samples from plants grown in the same environment (i.e., same geographic location). We observed separation of microbes in plant samples of the same species grown in different locations/environments. However, pooled samples across all species from the common garden with the same geographic origin (EA vs. ENA) showed a moderate level of dissimilarity in fungal endophytes between EA and ENA.  An overall significant correlation between endophyte community dissimilarity and phylogenetic distance was detected among the disjunct genera but not among species of Cornus. However, significant correlation between order, family, and genera of endophytes and phylogenetic distance of Cornus species was observed. We also found no significant differences in Foliar Endophytic Fungal (FEF) communities between counterparts of disjunct species pairs in EA and ENA in most genera except in Liriodendron and Cornus, although the beta diversity within genera is high. Our results suggest important roles of host identity and environment (geographic locations), and a likely minor role of phylogenetic divergence and biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera, as well as in Cornus. The results further suggest that the sister taxa in EA and ENA are likely different in their foliar endophyte composition when growing in their native habitats due to differences in geographic locations and local environments, which is potentially a factor driving allopatric divergence of species functional features. This hypothesis can be tested by analysis of samples from native habitats.