This study investigated indoor air quality (IAQ) at 39 public sites in southern Taiwan including hospitals, schools, office buildings, hypermarkets, libraries, railway stations, theaters, etc. Indoor air quality was preliminarily assessed using handy digital apparatus. Items detected include carbon dioxide (CO2), carbon monoxide (CO), formaldehyde (HCHO), total volatile organic compounds (TVOCs), total bacteria counts (TBC), total fungi counts (TFC), PM10, PM2.5, ozone (O3) and temperature. Based on the results of walk-through detection, the spatial distribution of indoor air contaminants was further measured over a 24 hour period using the EPA standard method. Major indoor air pollutants were found to include CO2, TBC, and TFC. The measured CO2 concentrations ranged between 438 and 1527 ppm, and only 38.9% of them met the Taiwan EPA suggested threshold of 600 ppm. In the schools and hospitals (Category 1), the measured TFC and TBC concentrations ranged from 62 to TNTC CFU/m3 and from 196 to 4875 CFU/m3, respectively. 33% TFC and 83% TBC concentrations exceeded the suggested threshold, and CO2 concentrations were moderately correlated with TBC levels. In a case study of hospital bioaerosols, high TBC and TFC levels were effectively lowered through disinfectant housekeeping as well as ClO2 spray. Three filamentous fungus genera were identified as Cladosporium perangustum, Cladosporium tenuissimum, and Fusarium incarnatum from outdoor samples with high TFC concentrations.