For good health, including fresh fruits and vegetables in our daily diet is very important. Fresh fruits and vegetables are highly perishable and affected by different microbial contaminants from production up to consumption. The objective of this study was to evaluate the important microbial spectrum of selected fruits and vegetables and their management from Hawassa town markets. A total of 27 fruit and 9 vegetable samples were analyzed for pathogens from their surface wash. The mean aerobic mesophillic count (AMC) ranged from 2.04x10 -7 cfu/ml to 4.2x10 -6 cfu/ml from the surface wash and the total coliform count (TC) ranged from 2.50 LTBc cfu/ml x10 -7 to 1.5x10 -6 cfu/ml. Fecal coliform ranged from 3.2x10 -6 to 0 cfu/ml and the range for Salmonella spp. and Staphylococcus aureus were 1.8x10 -6 to 0 cfu/ml and 2.50 LTBc x10 -7 to 0 cfu/ml respectively. Mold and yeast count ranged from 7.6x10 -6 to 0.2x10 -4 from the fruit surface wash. There was statistically significant difference regarding to AMC and TC between markets in between banana and orange samples and they were detected in all fruit samples. From the 36 samples E. coli and molds and yeast were found in all fruit samples, and Salmonella and Staphylococcus aureus were detected in 89% fruit samples in each. Activities during harvesting, transportation, storage and marketing conditions favored contamination of most commonly used fruits banana and orange. Besides, poor hygiene of the venders, using microbial unsafe containers, poor handling practice and poor environmental conditions such as sanitarily unsafe marketing environment were identified to be another sources of contamination. Hence, for safe and clean supply of fruits, community members working with the fruits must be trained on the ways by which fruits can be contaminated and the safe methods of harvesting, transportation, storage and vending the fruits.