The selected 21 public sites for indoor air quality (IAQ) investigation located at Penghu and Kinmen Islands (Taiwan). IAQ measurements include CO2, CO, HCHO, TVOCs, bacteria, fungi, PM10, PM2.5, O3 and temperature, which were conducted during year 2010 and 2011. The results showed that the concentrations of CO, HCHO, PM10 and PM2.5 were below Taiwan EPA's suggested IAQ threshold levels at all public sites. CO2 concentrations at hospitals and school are all exceeding category 1 threshold of 600 ppm. Besides, the levels of O3 and bacteria for hospitals and fungi for schools were all higher than the suggested IAQ threshold levels. One supermarket was found exceeding the suggested IAQ threshold levels on TVOCs and CO2. The theater was found exceeding the suggested bacteria threshold. This study discovered that the high CO2, bacteria and fungi levels occurred at various public sites. Accordingly, the regulated strategy of crowd control and air conditioning management was required for a healthy indoor environment.