Air borne fungi are transmitted through the air which can cause respiratory infections in human leading to allergies, asthma and diseases of the respiratory tract. The study is to determine the prevalence of fungi isolates in Enugu and Nsukka indoor prison environments and the possible effects on the respiratory tracts of the prison inmates. Institutions that accommodate large number of people such as Prisons, schools and hospitals are prone to airborne diseases due to overcrowded and unhygienic environment. The study was carried out using convenience sampling method and health based questionnaires. One hundred and forty (140)samples were analyzed consisting prison offices(48),inmates cells (28),lavatory (16),furniture(8),nasal swabs(20) and hostels(20). AC single impactor with high vacuum pump was used for indoor air sample collection; thermometer was used in measuring the temperature of the room and hygrometer for measuring the humidity. Sterile swab was used in collection of nasal samples, walls, furniture, toilets and bathrooms. Sabouraund dextrose agar (0.05µg Chloramphenicol and 1µg of Streptomycin), Malt extract agar, Chromagar, Brain heart infusion agar, and Nutrient agar were used for culture media for isolation of fungi respectively. The data generated from this research was analyzed using SPSS statistical software version 23.The result obtained showed that the percentage distribution of fungi isolates in prison offices were 60.9%, 57.4% in Nsukka and Enugu respectively while the percentage distribution percentage distribution of fungi isolates in prison cells were 42.6% and 39.1% in Enugu and Nsukka respectively. There was a significant difference in the distribution of fungal isolates at P=0.042.The indoor temperature and humidity of Enugu and Nsukka were the same at P using ANOVA, when compared with the hostels that served as control. Considering the public health effects of these airborne fungi, appropriate measures should be put in place in prison indoor environment to prevent the growth of moulds and yeast and its dissemination.