Habitat fragmentation affects lichen communities by inducing edge effects, although the dispersal of pollutants by pesticide drift from commercial crops may also provoke alterations in community structure, due to the varying sensitivity of lichen morphotypes to pollutants. In this context, we tested the hypothesis that lichen morphotype richness and diversity, and the percentage area of the trunks covered by different lichen morphotypes are modified significantly at the edges of fragments of Cerrado vegetation inserted within the agricultural matrix. We evaluated habitat fragments representing different Cerrado formations (Cerradão, Cerrado sensu stricto, and seasonal semi-deciduous forest) as well as the Emas National Park, a prominent Cerrado conservation unit. We used Generalized Linear Mixed Models (GLMMs) to test the potential of the models compiled using a mixture of phytosociological and environmental parameters, including the species, the height of the host plant (H), the circumference of its stem at breast height (CBH), total chlorophyll (TC), bark fissuring (BF) and pH, and illuminance (Lum), to explain the observed variation in the lichen morphotype richness and the percentage cover of the trunks by corticolous lichen morphotypes at the center and edge of the fragments. The central areas invariably had a greater diversity of morphotypes in all the fragments. The morphotypes considered highly sensitive to disturbance were not observed in edge areas, confirming a clear edge effect, as well as the influence of pesticide drift from the adjacent farmland matrix, on the structure of the lichen community. At both the edge and center sites, the larger trees (higher CBH) with less fissured bark tended to have the greatest diversity of lichen morphotypes, and more acidic barks had the greatest lichen cover. The models tested indicated that the variable tree species is an important determinant of the observed patterns of lichen morphotype richness and cover, either on its own or in association with pH or CBH + pH. The analyses also indicated that all the variables tested are important in some way for the definition of the percentage cover of the host trunks. The present study contributes to the understanding of the diversity of the corticolous lichen communities in the remaining fragments of Cerrado vegetation and the effects of the agricultural matrix on this community. The lichen may thus play a role as indicators of impact on other species, these organisms may provide important insights for the further investigation of the disturbance caused by the agricultural matrix on the communities of other groups of organisms.