Plant-microbe interactions have shaped the evolutionary pathways of both taxa, and hold promise for allowing these lineages to persist in the future. Microbes may function as a benefit to plants during harsh climatic years, which may allow more individuals to persist and reproduce under climate change. Through this buffering effect, we hypothesize that symbiosis may lead to more genetic diversity in plant populations. Currently, there are no studies assessing how microbial symbiosis impacts host genetic diversity. Using genotype-by-sequencing (GBS) data we quantified genetic diversity in paired endophyte-present and -absent plots of six native North American grasses from a ten-year long-term study. We calculated the average allelic diversity present in each plot. A type II ANOVA (Response variable ~ Endophyte Status * Species) was used to test if endophyte status was a significant predictor of allelic diversity. Endophyte status was a significant predictor of allelic diversity. All taxa when endophytes were present had higher averages of allelic diversity than when endophyte were absent. Further, our demographic data indicate demographic performance is more consistent in taxa with fungal endophytes. Through broadening our understanding of the impact host-microbe context-dependent interactions have on genetic diversity, we are better equipped to make predictions about maintenance of biodiversity under anthropogenic climate change.