Samples taken from sedimentary archives indicate that fungal non-pollen palynomorphs (NPPs) can be used to provide information on forest cover, fire regime, and depositional environment in the eastern Andean flank montane forest of Ecuador. Within the 52 samples examined, 54 fungal NPP morphotypes are reported, of which 25 were found to be previously undescribed. Examination of fungal NPPs over a gradient of forest cover (2–64%) revealed three distinct assemblages: (1) low (<8%) forest cover Neurospora, IBB-16, HdV-201, OU-102, and OU-110 indicative of an open degraded landscape; (2) medium (8–32%) forest cover Cercophora-type 1, Xylariaceae, Rosellinia-type, Kretzschmaria deusta, Amphirosellinia, Sporormiella, and Glomus suggestive of a forested landscape disturbed by herbivores and soil erosion; and (3) high (32–63%) forest cover Anthostomella fuegiana, OU-5, OU-101, OU-108, and OU-120. Environmental variables for forest cover (forest pollen), available moisture (aquatic remains), regional fire regime (microcharcoal), and sediment composition (organic carbon) were found to explain ~40% of the variance in the fungal NPP data set. Fire was found to be the primary control on fungal NPP assemblage composition, with available moisture and sediment composition the next most important factors.