Food losses and waste caused by mycoflora, develops on crops between harvesting and consumption. Reducing postharvest waste, especially in developing countries can be a sustainable solution to increase food availability and improve farmers livelihoods. Based on this, study was conducted during harvest to storage season of at Advance Plant Pathology Laboratory, Department of Plant Science and Biotechnology, University of Nigeria, Nsukka, to assess the mycoflora associated with post-harvest rot of onion and garlic. The two Allium species with signs of rot were collected from three different local markets in Nsukka, Enugu State, Nigeria. A total of seven mycoflora were isolated from the diseased onion bulbs while ten mycoflora were isolated from the diseased garlic bulbs. The fungal species isolated from onion bulbs were Aspergillus niger, A. flavus, A. fumigatus, A. terreus, Fusarium oxysporum, Penicillium citrinum and Rhizopus stolonifer while fungal species isolated from garlic bulbs were A. flavus, A. fumigatus, A. japonicus, A. niger, Botrytis allii, Fusarium oxysporum, Galactomyces candidum, Mucor racemosus, Penicillium citrinum and Rhizopus stolonifer. All the isolates in onion bulbs were present in garlic bulbs except A. terreus. Aspergillus niger had the highest frequency of occurrence of 33.78 and 32.79% in both onion and garlic, respectively. The least frequency of occurrence of 0.66% (A. terreus) and 1.09% (G. candidum) were also observed for onion and garlic. The pathogenicity test indicated that all the isolated fungi were pathogenic to their respective hosts. A. flavus with rot diameter of 38.67 mm and R. stolonifer with rot diameter of 35.00 mm were more pathogenic to onion and garlic bulbs respectively and significantly different from all the other isolates at P < 0.001. A. flavus was more severe on the 6th day of incubation of onion bulb while R. stolonifer was more severe on the 5th day of incubation of garlic bulb. This research has shown that mycoflora associated with the rot of onion and garlic bulbs could lead to their post-harvest losses, this should necessitate pre and post harvest strategies in order to mitigate the effects of these pathogens.