Fruits are colonized by fungi, bacteria and other agents causing different types of disease. Fruits, due to their low pH, high moisture content and nutrient composition are highly susceptible for the colonization of pathogenic fungi and bacteria. Microorganisms associated with decaying of stored fruits were studied using standard Microbiological methods. The analysis was done with Papaya, Banana, Guava, Orange, Apple, Custard apple, Mango, Sweet lime, Lemon, Gooseberry, Pomegranate, Pear and Grape. Aspergillus species (42%) had the highest rate of occurrence among the isolated fungi, followed by Candida species (36%) while Penicillium spp. (13%), Rhizopus spp. (6%) and Mucor spp. (3%) were the least predominant. It also showed that of the three bacterial species isolated from fruits, Klebsiella pneumoniae was highest (50%) followed by Pseudomonas aeruginosa 29% and Escherichia coli was the least (21%). It showed that fungal isolates were most predominant compared to the bacterial isolates. This investigation was undertaken to find out the association of fungi and bacteria with the decaying fruits from Thiruporur of Kancheepuram district and to identify them.