One hundred five species of lichenized and allied fungi are reported from recent and historical collections made in the Mitchell Mill State Natural Area in northeastern Wake County, North Carolina, USA. Mitchell Mill is unique among granitic flatrock communities in the southeastern United States by having riparian elements from the Little River, which flows directly over the flatrock, supporting semi-aquatic lichen communities along creek edges represented by species in Dermatocarpon, Verrucaria, and Lichinales. Recently described or renamed species Cladonia ignatii, Lecanora provertula and Phyllopsora isidiosa were found in recent collections. Compared to historical records, 38 taxa including five of six species of large cyanolichen were not found in recent visits, indicating a loss of diversity over the past 100 years, likely due to human activities.