Eggs are perishable and fragile foods because of their easy contamination by different microorganisms, such as fungi. Hence, research on egg safety and quality has been recently developed worldwide to minimize illness transmitted by this food, although most present mainly pathogenic bacteria. Thus, this study identified potentially pathogenic fungal species in eggshells from free-range and commercial hens offered in supermarkets in Fortaleza, CE, Brazil. The research was performed at the Vettings laboratory at the State University of Ceará (UECE) with 40 eggs: 20 from commercial and 20 from free-range hens. The eggshells were assessed using the dextrose evaluation method for pathogenic cultivation, commensal, and yeast fungi. Subsequently, readings were taken to identify and count the fungi on a binocular light microscope in 100x increments. Both egg categories showed a significant number of colony-forming units (CFU). The study identified eight different fungal species in both egg production types. The most prevalent fungal colonies in the free-range hen lineage (brown shell) were yeast spp. and Penicillium citrinum, and the laying hen lineage (white shell) had mostly Penicillium spp. and yeast spp. Therefore, both egg production systems showed similar fungal contamination, which suggests that the manipulation and/or storage are adequate despite the lack of strict food safety regulations or supervision for eggs in Brazil.