Little is known about the diversity and ecological roles of endophytes in woody roots of forest trees in the inland northwestern USA, especially as related to fire ecology. To assess fungal endophytes in large woody roots of Douglas-fir (Pseudotsuga menziesii) and ponderosa pine (Pinus ponderosa), we conducted a mycobiotic survey of root-core samples from 12 sites in north-central Washington State. Each site was subjected to one of the following fuel treatments: 1) untreated control; 2) burn only 3); thin only; and 4) thin and burn. Fungal endophytes were cultured and identified by morphology and sequencing of ITS1, 5.8S, ITS2 rDNA. In total, 1130 surface-disinfected, root-cores pieces were processed and 43% yielded one or more fungal isolates. From the 1130 surface-disinfected, root-cores pieces, 365 (72%) of 509 fungal isolates were identified comprising 20 genera (224 isolates) of hyphomycetes, 5 genera (79 isolates) of Ascomycota, 3 genera (48 isolates) of Zygomycota, and 14 isolates of Basidiomycota. Among the more interesting findings were 1) yeast taxa usually associated with above-ground bark beetles including two undescribed species of Candida; 2) a putatively undescribed eurotiaceous fungus that produces ascomata in culture; and 3) multiple genera of dematiaceous hyphomycetes that have been reported from above-ground plant tissues and grass roots. Fuel treatment, host species and culture media all significantly influenced fungal endophytes recovered. Compared to controls, units subjected to burn-only showed reduced numbers of fungal endophytes; whereas recovery of endophytic fungi increased in the thin and burn units and thin-only units exhibited no change. Some associations are noted among tree root endophytes, grass root endophytes, and above-ground saprobes and facultative parasites, because many of the same species are found across all of these habitats and environments. Possible roles and functions of endophytic fungi of woody coniferous roots are discussed.