Fruits and vegetables provide an ideal condition for the growth of microorganisms. They contaminate fruits and vegetable and made them insufficient for consumption. Many fungal and bacterial species are responsible for the spoilage of fruits and vegetables. In our present study, an investigation has been carried out to isolate and identify the fungal and bacterial species which are responsible for the spoilage of some fruits and vegetable particularly apple, grapes and tomato. Samples of contaminated fruits and vegetables were collected from three different markets (Tezpur Bazaar, Mission Chariali Bazaar and Poruwa Bazaar) and were immediately surface sterilized and studied.10 fungal isolates were found to be most commonly occurring in all of the samples, Similarly many isolates of bacteria were found to be common contaminants from the three samples. Biochemical tests and viable bacterial counts (10-2)/g of sample was also calculated.