The population diversity within isolates of Glomerella cingulata and Colletotrichum spp. associated with Glomerella leaf spot and bitter rot of apples was studied in an orchard of cv. Granny Smith located in Wilkes County, NC, and one orchard each of cultivars Granny Smith and Gala located in Lincoln County, NC. Morphological characters and vegetative compatibility groups (VCGs) were used to determine diversity within the species. The relative frequencies of the morphological types found within each species in each orchard were also determined. G. cingulata was the predominant species associated with bitter rot in the three orchards and Glomerella leaf spot in the Gala orchard. In the three orchards, different morphological types were observed within isolates of G. cingulata and Colletotrichum acutatum, but not within isolates of Colletotrichum gloeosporioides. Isolates of C. gloeosporioides were not found in the orchard of cv. Granny Smith in Lincoln County. In the other two orchards, C. gloeosporioides represented the lowest proportion of the population. Three VCGs were found among isolates of G. cingulata (VCG-1, 2, and 6), two among isolates of C. gloeosporioides (VCG-9 and 10), and two among isolates of C. acutatum (VCG-15 and 16). VCGs 2, 6, 9, 10, 15, and 16 were found in the Granny Smith orchard in Wilkes County, VCGs 1, 2, and 6 in the Gala orchard in Lincoln County, and VCGs 2 and 6 in the Granny Smith orchard in Lincoln County. Differences in frequencies among the different morphological types found within the three orchards remained relatively similar throughout the season and from year to year, suggesting that the relative frequencies of G. cingulata, C. gloeosporioides, and C. acutatum remain stable in an orchard once the fungi are established.