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Abstract Nearly all plants are colonized by fungal endophytes, and a growing body of work shows that both environment and host species shape plant-associated fungal communities. However, few studies place their work in a phylogenetic context to understand endophyte community assembly through an evolutionary lens. Here, we investigated environmental and host effects on root endophyte assemblages in coastal Louisiana marshes. We isolated and sequenced culturable fungal endophytes from roots of three to four dominant plant species from each of three sites of varying salinity. We assessed taxonomic diversity and composition as well as phylogenetic diversity (mean phylogenetic distance, MPD) and phylogenetic composition (based on MPD). When we analyzed plant hosts present across the entire gradient, we found that the effect of the environment on phylogenetic diversity (as measured by MPD) was host dependent and suggested phylogenetic clustering in some circumstances. We found that both environment and host plant affected taxonomic composition of fungal endophytes, but only host plant affected phylogenetic composition, suggesting different host plants selected for fungal taxa drawn from distinct phylogenetic clades, whereas environmental assemblages were drawn from similar clades. Our study demonstrates that including phylogenetic, as well as taxonomic, community metrics can provide a deeper understanding of community assembly in endophytes.