Background: Air pollution by fungal spores poses a potential threat to the health and wellbeing of people. Airborne Aspergillus species play an important role in causing allergenic and invasive infections in susceptible individuals. Objectives: We conducted this study to determine the prevalence and pathogenic potentials of airborne Aspergillus species in homes, offices and hospitals in Northern part of Anambra State. Methodology: A total of 420, 70 and 59 air samples were collected from homes, offices and hospitals respectively using A6 single stage air sampler. Nasal swabs of occupants of same indoor environments were examined. Results: The pathogenic potentials of some isolates in immunocompromised and immunocompetent Balb C mice were investigated using pharyngeal aspiration technique. Some of the fungal isolates were subjected to molecular studies to establish the similarity between air and nasal isolates. Twelve species of Aspergillus were recovered from homes and hospitals while 11 species were recovered from offices. Aspergillus niger was the predominant fungus (76.6%, 61.4%, 62.7%) followed by A. fumigatus (51.4%, 34.2%, 38.9%). Consequently A. niger was the dominant fungus in the nasal swabs of occupants of these environments (homes 66%, offices 19% and hospitals 14%). Immunosuppressed Balb C mice inoculated with spores of A. fumigatus died 51, 54 and 58 hours after inoculation while mice inoculated with A. niger developed lesions on the lungs. Conclusion: DNA sequence of airborne A. niger and A. niger from nasal swab of occupant of same environment showed genetic relationship. Considering the presence of fungi with pathogenic potentials, environmental monitoring is necessary to prevent possible infection.