Heavy metal pollution poses a serious hazard to human health, and microbial remediation of heavy metals in soil has been widely studied. A group of ascomycetes classified as dark septate endophytes (DSEs) colonize plant roots and benefit host plants under abiotic stress conditions. In this study, Phragmites australis, a common remediation plant in Baiyang Lake, was investigated. The root system and soil of P. australiswere collected in typical heavy metal-contaminated sites, and the species diversity and community structure of DSEs in P. australisroots were studied. In addition, DSE strains were isolated, cultured, and tested for their tolerance to Cd stress. The results showed that DSEs occur extensively in P. australisroots, forming typical dark septate hyphae, with a total colonization rate of 19.7–83.1%. Morphological and ITS sequencing analyses were used to identify 10 DSE fungi in 9 genera. Among these fungi, 6 strains with considerable resistance to Cd stress were identified. The biomass values of Poaceascoma helicoides, Alternaria doliconidium, and Acrocalymma vagumstrains increased as the Cd concentration increased. These results can not only help to understand plant-DSE interactions in wetland environments, but also provide a theoretical basis for making full use of DSE fungi to alleviate heavy metals in soil.