Certain species of foliar fungal endophytes found in conifer trees produce anti-insect compounds. Seedlings inoculated with these toxigenic endophytes have increased tolerance to the spruce budworm, Choristoneura fumiferana. To facilitate the detection of the fungi in tree samples, polyclonal assays were developed for the pyrenophorol-producing endophytes Lophodermium nitens CBS127939, Lophodermium nitens CBS127941 and Lophodermium cf. piceae CBS127942. LOQs were found to be 50 ng of mycelium for each assay. qPCR assays were developed for the rugulosin-producing endophyte Phialocephala
scopiformis DAOM229536 and pyrenophorol-producing endophytes Lophodermium nitens CBS127939 and Lophodermium nitens CBS127941 based on the ITS region of fungal ribosomal DNA targeting genetic polymorphisms unique to those strains. LOQs were found to be 100 ng, 10 ng and 10 ng of mycelium/gram of needle, respectively. The qPCR method was found to be more sensitive, detecting the endophytes in 48% of tree samples. The polyclonal assay detected endophytes in 7% of samples.