Wild birds play a significant role in the dissemination of micro-organisms, including fungal agents, through feathers, skin debris, and feces, both locally and across regions via migration. Identifying fungal carriage in wild birds is crucial for understanding the prevalence of pathogenic fungi and developing effective strategies to prevent and control mycotic infections. This study investigated fungal carriage in wild pigeons, doves, water birds, birds of prey, and small passerines in Balıkesir province of Türkiye, an ecologically important region characterized by key wetlands, two national parks, and major migratory bird routes. A total of 46 wild bird samples were analyzed by culture method, as the “gold standard”, and several clinically important fungal isolates were obtained and subsequently further analyzed by PCR. Fungi were detected across all bird categories, with 27 birds (58.70%) testing positive for at least one fungal species. In total, 10 distinct fungal taxa were isolated from the wild birds. The most frequently identified organisms were Mucor spp. (28.26%) and Aspergillus niger (6.52%), followed by Sporothrix schenckii (4.35%), Candida glabrata (4.30%), Arthroderma terrestre (2.17%), Trichophyton mentagrophytes (2.17%), Nannizzia gypsea (2.17%), Aspergillus flavus (2.17%), Aspergillus fumigatus (2.17%), Lichtheimia spp. (2.17%), and Beauveria spp. (2.17%). Prevalence was the highest in birds of prey and small passerines (77.78%), moderate in pigeons and doves (58.82%), and the lowest in water birds (27.27%). These results emphasize the role of wild birds as potential reservoirs and vectors of fungal agents, highlighting the importance of continued surveillance and biosecurity measures to mitigate the risk of environmental and zoonotic transmissions.