During the summers of 2005 and 2006, northern flying squirrels (Glaucomys sabrinus Shaw) were live-captured in the northern Black Hills of South Dakota from mixed deciduous/coniferous and coniferous habitats. Squirrel captures were significantly correlated with volume of downed wood and number of snags. Diets were examined from scat collections (n = 40, deciduous/coniferous; n = 10, coniferous). Number of fungal spores in the scat was significantly correlated with number of snags. From each scat collection, the frequencies of plant, animal, fungal, and unidentified components were determined. Hypogeous fungi were a frequent component of the diet, being found in 98.3% and 78.8% of the scat observed in 2005 and 2006. In 2006, as the frequency of dietary fungi decreased, the frequency of plant material increased from <1.0% to 8.0% and frequency of unidentified material increased from 2.0% to 74.0%. Animal content in the scat was negligible (<1.0% to 1.0%) Rhizopogon was the most frequently occurring hypogeous fungus observed. Rhizopogon spores made up 97.9% of the spores counted in 2005 and 96.4% in 2006. Elaphomyces, Gautieria, Geopora, Hymenogaster, and Hysterangium were observed at much lower frequencies. Sporocarps were collected throughout the trapping periods. Fourteen were collected in 2005 and 12 in 2006. Of the 26 sporocarps collected, 11 were Rhizopogon, 4 Elaphomyces, 2 Gautieria, 1 Hymenogaster, 7 Hysterangium, and 1 Tuber. This study is the first to examine flying squirrel diets in the Black Hills and the first to report Elaphomyces, Gautieria, Hymenogaster, Hysterangium, Rhizopogon, and Tuber sporocarps from the South Dakota Black Hills.