Aim: The study was carried out to isolate and identify Aspergillus species from commercial birds with suspected aspergillosis in the poultry farms within Ado Ekiti metropolis Nigeria.  Place and Period of Study: The study was carried out in the Department of Microbiology, Faculty of Science, Ekiti State University Ado Ekiti, Nigeria in August 2016. Methodology: A total of 35 sick/suspected birds were collected randomly from three poultry farms. At Ago-Aduloju poultry farms, 15 samples were randomly collected from 1000 birds while at Ekiti State University poultry farms, 10 samples were randomly collected from 500 birds. At Federal Polytechnic Ado Ekiti poultry farms, 10 samples were randomly collected from 700 birds. The bird’s selection was on the basis of clinical signs and symptoms such as difficulty in breathing, weight loss, drooping of wings and exercise intolerance. Swab samples were collected from each suspected/sick bird for mycological culture and molecular characterization of the isolates from each bird was carried out. The isolates were identified based on the color of the culture on Potato Dextrose Agar and microscopic examination. Molecular identification was done using 23S Ribosomal RNA Gene and Partial Sequence. Results: Six fungal strains that showed similar morphological and cultural characteristics of Aspergillus species were isolated. The isolates were coded ASP 1, ASP 2, ASP 3, ASP 4, ASP 5, and ASP 6. The identified organisms were; Aspergillus fumigatus qH 107 (ASP 1), Aspergillus fumigatus qH 107 (ASP 2), Aspergillus flavus M09 (ASP 3), Aspergillus flavus UOMS6 (ASP 4), Aspergillus fumigatus qH 107 (ASP 5), Aspergillus flavus qH 107 (ASP 6). Conclusion: It is evident that Aspergillus species were predominant in poultry farms selected in this study. Necessary precaution should be put in place to prevent the spread of aspergillosis. Poultry farmers are advised to avoid damp environments, moldy feeds, dry and dusty litters. Adequate ventilation should always be provided in poultry farms to prevent Aspergillosis.