Indoor environmental quality has gained attention in the past decades due to the increased periods of time spent enclosed in buildings. Parameters such as ventilation, water damage, type of paints used, use of carpets, etc. affect the indoor air quality significantly. With the rising concern regarding outbreaks and pandemic, it is important to investigate the microbial load and consortium structure in schools. This thesis aims at determining the microbial loads in three selected schools in the Balçova District of İzmir, Türkiye. Two sampling campaigns were conducted, one in the winter break (February 2022) and one in the spring semester (May 2022). Surface swab samples and settle-plate air samples were collected from pre-defined spots at schools. Surface swab samples and settle-plate air samples were examined via both classical microbial culture methods and modern DNA analysis methods. Via classical microbial culture methods, culture comparison from the database, fungi cultures were dedicated up to genus level. Via modern DNA analysis method, Sanger sequencing, bacterial cultures were dedicated up to genus level too. All the results indicated that three schools were hosting possibly dangerous genera of both fungi and bacteria. But, this also showed that genus-level discrimination is still not enough to utter exact indoor air quality from the perspective of indoor microbiota to the identification of possible health risks for occupants. For further studies, microbial mapping should discriminate up to species level to demonstrate exact indoor air quality and indoor microbiota vie high throughput sequencing methods.