Onion (Allium cepa L) is extremely important vegetable crop not only for internal consumption but also as highest foreign exchange earner among the fruits and vegetables. Maharashtra is India’s top onion producing state accounting for one-third of the total annual onion production of 16 million tonnes. Onions (Allium cepa L.) are commercially valuable and important seasonal crop of Maharashtra (India), Onion (Allium cepa L.) is one of the important vegetable and consumed daily as a flouring agents. The characteristics aroma and odor of onion is due to allicin (diallylthiosulfate), which accounts for its use as medicine, food, salad, spice, and condiment in the Indian foods. Many fungi are responsible for the deterioration of onion bubs due to improper handling and storage practices. The aim of the present investigation is to find out the fungi responsible for the deteriorating of onion in post harvest conditions. The onion bulbs were collected from different markets of Mumbai (India) and screened aiming to record the incidence of fungi responsible for the deterioration of Onion bulbs during storage in different seasons. The investigation revealed that four major fungal species were prevalent on Onion bulbs. viz. Aspergillus niger, A. flavus, Penicillium sp. and Rhizopous stolonifer. A. niger and Penicillium sp. were the most dominated and frequently isolated fungi. Considering abundant host range and worldwide distribution of these fungi, common management strategy may not be effective. There is no statistical relationship established between the samples collected from different markets and the different climatic conditions (seasons). In all seasons the dominant fungi were present in the samples collected from different markets. This article will be helpful for providing information about integrated disease management of associated fungal disease of onion during post harvest condition and in various aeromycological investigations.