This is the first study to assess fungal diversity and mycotoxigenic fungi in open recirculating cooling-tower (CT) water systems (biofilm and water phase). The production capability of mycotoxin from fungal isolates was also examined. The mean fungal count in 21 different water and biofilm samples was determined as 234 CFU/100 mL and 4 CFU/cm2. A total of 32 species were identified by internal transcribed spacer (ITS) sequencing. The most common isolated fungi belonged to the genera Aspergillus and Penicillium, of which the most prevalent fungi were Aspergillus versicolor, Aspergillus niger, and Penicillium dipodomyicola. From 42% of the surveyed CTs, aflatoxigenic A. flavus isolates were identified. The detection of opportunistic pathogens and/or allergen species suggests that open recirculating CTs are a possible source of fungal infection for both the public and for occupational workers via the inhalation of aerosols and/or skin contact.