Endophytes are microbes that live, for at least a portion of their life history, within plant tissues. Endophyte assemblages are often composed of a few abundant taxa and many infrequently-observed, rare taxa. The ways in which most endophytes affect host phenotype are unknown; however, certain dominant endophytes can influence plants in ecologically meaningful ways--including by affecting growth and contributing to immune responses. In contrast, the effects of rare endophytes have been unexplored. Here, we manipulate both the suite of rare foliar endophytes and Alternaria fulva--a dominant, heritable fungus--within the Fabaceous forb Astragalus lentiginosus. We report that rare endophytes, despite likely occupying only a small amount of host tissue, affected host size and foliar %N, but only when the dominant fungal endophyte (A. fulva) was not present. A. fulva also reduced plant size and %N, but these deleterious effects on the host could be offset by a striking antagonism we observed between this heritable fungus and a foliar pathogen. These results confirm that interactions among taxa determine the net effect of endophytic assemblages on their hosts. Moreover, we suggest that the myriad infrequently-observed endophytes within plant leaves may be more than a collection of uninfluential, commensal organisms, but instead have meaningful ecological roles.