Thin-layer chromatography (TLC) analysis indicated that three strains S-1, S-2, and S-3 of endophytic fungi isolated from roots, stems and leaves of Spiranthes sinensis could produce flavonoid. To identify these 3 strains, ITS DNA regions of 3 strains were amplified through PCR reaction and sequenced. The phylogenetic tree was constructed by the software MEGA (version 4.0) using Neighbour-joining methods. Morphological observation and molecular biology identification indicated that the strain S-1 was Curvularia inaequalis., and S-2 and S-3 were Penicillium pinophilum.