Little is known about hypogeous, sequestrate fungi (i.e., truffles) in the eastern United States. Since the fruiting bodies of these fungi are part of the diet of multiple rodent species, filling data gaps is important to understanding more about truffle species distribution and habitat associations. During a microhabitat study on radio-collared Glaucomys sabrinus fuscus (Virginia Northern Flying Squirrel) in 2013, we opportunistically sampled truffles at small-mammal digs and scratches within our microhabitat plots. All sampling was conducted within known squirrel-foraging home ranges. We found 3 Elaphomyces species: E. macrosporus, E. verruculosus, and E. americanum. Our observations of E. macroporus are the first from West Virginia. Herein, we describe the microhabitat associations for each fungal species. We suggest using small-mammal digs and scratches as potential indicators to opportunistically gather more information on truffle species in coniferous forests of the eastern United States.