The widespread aquatic plant Persicaria amphibia (water smartweed, Polygonaceae) occurs in both flooded aquatic habitats and moist terrestrial environments. Its physiological versatility and wide geographic range highlight its resilience to stress and make the species intriguing for the study of fungal endophytes. Endophytes occur within living plant tissues and are known from diverse aquatic, marine, and terrestrial plants, where they often mitigate plant responses to stress. As part of a study evaluating endophyte communities associated with aquatic plants in lentic waters of Arizona, USA, we isolated a distinctive clade of endophytes from healthy, living roots of seasonally inundated P. amphibia, which we describe here on the basis of morphology and evidence from four loci as new species Clohesyomyces symbioticus (Lindgomycetaceae, Pleosporales, Dothideomycetes, Ascomycota). Clohesyomyces has long been considered a monotypic genus comprising the saprobic species C. aquaticus, presently known from submerged wood in freshwater systems in Asia and Australia. Description of Clohesyomyces symbioticus highlights the occurrence of endophytism in this genus and expands its geographic scope to the western hemisphere.