To evaluate the indoor air quality of food manufacturing plants, the presence of viable bacteria and fungi was assessed in the indoor air of the facilities at which 9 food items were manufactured. Air samples were collected from the general zone, low clean zone and clean zone of each factory with an air sampler, in combination with plate counts agar using for bacteria, and dichloran-glycerol agar for fungi. The samples were incubated at $25^{circ}C$ for 4 to 7 days. After culture, the colony forming units (CFU) on each plate were counted and corrected with a positive hole conversion table. The average concentration of bacteria was $2.2{ imes}10^3;CFU/m^3$ in the general zone, $1.2{ imes}10^3;CFU/m^3$ in the low clean zone and $7.3{ imes}10^2;CFU/m^3$ in the clean zone. The average concentration of fungal microbes was $2.5{ imes}10^3;CFU/m^3$ in the general zone, $2.6{ imes}10^3;CFU/m^3$ in the low clean zone, and $2.0{ imes}10^2;CFU/m^3$ in the clean zone. No meaningful differences were detected between the general zone and the low clean zone, but the clean zone had significantly lower concentrations than the other zones. Additionally, the identification of the fungi was performed according to morphological method using a giant culture and slide culture. The fungi were identified as belonging to 18 genera, and the genera Cladosporium(33%), Penicillium(29%) and Aspergillus(26%), predominated. Aspergillus isolates were identified to species level, and A. ochraceus, a mycotoxigenic species, was identified. As part of the effort to control the quality of the indoor air of food manufacturing plants, our results show that continued studies are clearly warranted.