One new record of endophytic fungus, Truncatella angustata, in roots of Cypripedium tibeticum and C. bardolphianum, was reported in this paper. 148 strains of Truncatella angustata were isolated from the roots of C. tibeticum and C. bardolphianum as endopytes at different altitudinal areas in Huanglong Valley, Sichuan Province, China. Morphological descriptions of T. angustata revealed that the colony on PDA pale yellow, reverse of the culture yellowish brown; pycnidia black, pustulelike; conidia fusiform, 4celled, 3septate; apical appendages 1-5. Three genotypes (HLIO15_15a_22, HLIO15_20a_42 and HLIO15_17a_46) were identified by ITS rDNA analysis. The isolation rate of T. angustata was highest in the highest altitude population, containing all three genotype strains. The phylogenetic tree of the ITS sequence of the genus Truncatella was constructed. It was found that the strains with different ecological functions of the genus Truncatella did not form obvious clades.