Endophytes may play important roles in phytoremediation; however, little information is available on the endophytes of phosphorus (P)-accumulating plants and their potential application in P-phytoextraction. Here, 30 endophytic fungi were isolated from Polygonum hydropiper and classified into 24 taxonomic groups, with 76.7% being Ascomycota and 23.3% being Basidiomycota. Metarhizium anisopliae, Guignardia mangiferae and Phaeophlebiopsis peniophoroides were the dominant species. The Simpson and Shannon diversity indices were higher in shoots than in roots. The isolates had varied plant-growth-promoting traits with all being indole-3-acetic acid positive and only 18 exhibiting siderophore activities. P solubilization capability varied with fungal species and P sources; it correlated negatively with pH but positively with organic acids in a tricalcium phosphate medium. However, in a phytin medium, it did not correlate with pH, but positively with phosphatase activities. Five endophytes were found to have the greatest potential as inoculants to assist P. hydropiper in future P-phytoextraction studies.