Abstract: Tailing ponds are special growth environment for plants. Soils at such sites contain high concentrations of heavy metals, which affect the physiology and ecology of plants. The aim of this study was to evaluate the endophytic fungi resources at a copper mine tailings site, and to explore whether different endophytic fungi can restore diversity by altering the physical and chemical properties of soil. Therefore, we studied endophytic fungi of Bothriochloa ischaemum growing in the Shibahe tailings pools at the Tongkuangyu Mine, a copper tailings site. B. ischaemum is the dominant species growing at this site, and it grows in several sub-dams with different recovery times. To investigate the endophytic fungi infection rate of B. ischaemum, we collected live plants and separated the endophyte from the sheath, and observed and described the characteristics and spore morphology of each fungus. We also selected 16 strains and amplified the 5.8S-ITS region for sequencing and phylogenetic analysis. Based on their phenotypes, the endophytes from B. ischaemum growing in four different sub-dams with different recovery times were separated into different groups. Most endophyte colonies were white, and the growth rate ranged from 5.515 and 12.548 mm/d. The endophytes produced spherical or oval/near oval spores, with sizes ranging from 2.085 μm to 7.072 μm. Sequence analyses showed that there were three different sequences among the 16 kinds of colonies, belonging to the genera Gibberella, Fusarium, and Penicillium. The smallest genetic distance was between the sub-dam with 30-years recovery and that with 5-years recovery. The largest genetic distance was between the sub-dam with 45-years recovery and that with 15-years recovery. At copper tailings sites, different soil environments at different stages of restoration might lead to a wide diversity of endophytes infecting B. ischaemum. The results of this study provide a theoretical basis for enriching endophyte resources, and reveal some of the ecological functions of endophytes associated with B. ischaemum at a copper tailings site.