The aim of this study was to assess the microbial indoor air quality of primary and secondary schools in Obio- Akpor and Emohua Local Government Areas in Rivers State, Nigeria. Three public and three private schools were sampled. Air samples were collected using the gravitational sedimentation method. The samples were analyzed for the presence of bacteria and fungi, using Nutrient agar and Potato dextrose agar respectively. The bacterial population in the classroom and toilets ranged from 983-5899 CFU/m3 and 786-2751 CFU/m3 respectively, while the fungal population ranged from 1336-2319 CFU/m3 and 786-2637 CFU/m3. The bacteria isolated were identified as belonging to eight genera: Bacillus, Chromobacter, Escherichia, Lactobacillus, Micrococcus, Pseudomonas, Serratia and Staphylococcus, with Bacillus and Staphylococcus occurring more frequently. The fungal isolates were identified as belonging to eight genera: Alternaria, Aspergillus, Candida, Cladosporium, Microsporum, Mucor, Penicillium, with Rhizopus; Aspergillus and Mucor occurring more frequently. Some of the isolates identified in this study are of public health significance capable of causing respiratory disorders, bacteremia, pulmonary allergic diseases and gastrointestinal infections. Therefore, it is recommended that schools should maintain proper sanitary practices, maintain good ventilation systems and have less populated classrooms.