Air contains large number of microorganisms including bacteria and fungi and their estimation is important as an index of cleanliness for any particular environment. It becomes imperative to undertake a study of the microbiological air quality of the airborne micro-flora in the environments of two major government hospitals, University of Benin Teaching Hospital (UBTH) and Central Hospital, in Benin City metropolis. Both indoor and outdoor air samples were assessed monthly for the three (3) months in the wet season (June – August, 2010) and dry season (November 2010 - January 2011) using the settled plate methods. The study sites were divided into nine (9) units which include accident and emergency ward, laboratory, male ward, female ward, children ward, labour room, treatment room, theatre and outside the hospital gate. The mean airborne bacterial load in the two hospitals ranges from 8.5cfu/min to 172.5cfu/min and 5.5cfu/min to 64.5cfu/min for UBTH and Central hospital in the wet season. While the mean airborne fungal load in UBTH and Central Hospital in dry season ranges from 2.5cfu/min to 9.5cfu/min and 1.5cfu/min to 19.0cfu/min respectively. The female ward, children ward, accident and emergency ward and outside the hospital gate recorded the highest airborne micro-flora. The result revealed the isolation of ten (10) fungal isolates and six (6) bacterial isolates. These include Aspergillus niger, Aspergillus flavus, Botryodiplodia acerina, Rhizopus stolonifer, Nigospora zimm, Mucor sp., Monilla infuscans, Penicillium sp., Candida sp. and Trichoderma viridis while the six (6) bacterial isolates include Staphylococcus aureus, Staphylococcus epidermidis, Bacillus cereus, Bacillus sp., Serratia marcescens and Micrococcus sp. The result shows the highest fungal population of 26.5cfu/min (outdoor) in UBTH followed by 24.0cfu/min (outdoor) in Central Hospital. The highest bacterial load of 172.5cfu/min (outdoor) was recorded in UBTH. The fungal isolates Aspergillus niger (53.0%) and Monilla infuscans (43.9%) were showed to be the most frequently isolated airborne fungal organisms while Staphylococcus aureus (91.3%) and Staphylococcus epidermidis (85.8%) were the most frequently isolated bacterial isolates. The statistical analysis showed no significant difference between the microbial population obtained during the wet and dry seasons in both hospitals studied. Data generated underline the usefulness of monitoring hospital environments.