In this study an attempt was made to evaluate the qualitative and quantitative fungal burden (load) in five different working environments of South Assam (India) and the possible risks of indoor fungi to employees and stored products. Fungal concentrations in different working environments were studied using a Burkard personal petriplate sampler. The survey was done in five different working environments for one year. A total of 76 fungal types were recorded in the indoor air of South Assam during the survey period. The maximum fungal concentration (5,437.6 ± 145.3 CFU m−3 air) was recorded in the indoor air of medical wards, followed by the paper-processing industry (3,871.7 ± 93.4 CFU m−3 air). However the lowest concentration was observed in the indoor air of a bakery (1,796.8 ± 54.4 CFU m−3 air). The most dominant fungal genera were Aspergillus (34.2%) followed by Penicillium (17.8%), Geotrichum (7.0%) and the most dominant fungal species were Aspergillus fumigatus (2,650.4 CFU m−3 air) followed by Aspergillus flavus (1,388.2 CFU m−3 air), Geotrichum candidum (1,280.3 CFU m−3 air), Aspergillus niger (783.3 CFU m−3 air), and Penicillium aurantiovirens (774.0 CFU m−3 air). The fungal species viz., Aspergillusfumigatus, Penicilliumaurantiovirens, Aspergillusflavus, Aspergillusniger, Geotrichumcandidum, and Penicilliumthomii, which were recorded well above threshold levels, may lead to adverse health hazards to indoor workers. Setting occupational exposure limits for indoor fungal spores as reference values is obligatory for prevention and control of adverse effects of indoor fungal exposure.