Onion (Allium cepa L.) is a highly nutritive vegetable with about 2 million metric tons grown annually in Nigeria, but the majority is lost to postharvest spoilage, especially through microbial infection. In this study, we identified bacteria and fungi associated with postharvest spoilage in onion bulbs and determined the pathogenicity of the bacterial isolates. Two weeks stored onion bulbs were purchased at a market in Ile-Ife, rinsed in 5% HOCL and aseptically cut into seven sections each. The fourteen sections obtained were swabbed daily with sterile cotton-tipped applicators for seven days. The swabs were streaked onto the surface of Nutrient Agar (NA) and selective/differential media plates for the isolation of bacteria, and Potato Dextrose Agar (PDA) plates for the cultivation of fungi. The bacterial plates were incubated at 37°C for 24 hours, while the fungal plates were incubated at 25°C for 5 days. The isolates were identified based on standard microbiological methods. Pathogenicity tests of the bacterial isolates from each of the genera was carried out by re-inoculation on the inner tissues of fresh onion bulbs that have been cleaned with 1% NaOCL, an uninoculated onion bulb served as the control. Thirty-five (35) bacterial isolates belonging to four different genera were identified, which included; 11 (31.4%) Staphylococcus spp., 9 (25.7%) Micrococcus spp., 8 (22.9%) Bacillus spp. and 7 (20%) Flavobacterium spp. Seven (7) fungal isolates were identified which included; 5 (71.4%) Aspergillus fumigatus, 1 (14.3%) Gibellula suffulta and 1 (14.3%) Hirsutella saussueri. Pathogenicity tests revealed that all the bacterial isolates were able to cause rot in onion in comparison with the control which had no observable rot; Flavobacterium spp. (28 mm) was the most pathogenic, while Micrococcus spp. was the least pathogenic (14 mm) based on the diameter of rot formation within seven days. These findings revealed that spoilage microorganisms can cause onion rot, hence, onions already showing contamination symptoms should be separated from fresh ones to avoid cross-contamination, while adequate care should be taken before consumption of onion to avoid foodborne illnesses and diseases.