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Rotted apples collected from six cold stores and two fruit markets in Peshawar and Swat divisions showed attacks of Penicillium expansum (74.2%), Alternaria alternata (11.6%) and Rhizopus sp. (14.2%). However, P. expansum was found to be the most prevalent fungus both in apple stores and markets because of its survival potentiality both at low and high temperatures. These fungi are mostly wound pathogens and require injury for infection. The apple variety Red delicious was more susceptible to the disease than Golden delicious indicating differential reaction of these varieties to apple rot. However, the amount of rotting incited by Rhizopus sp. was greater than the other fungi due to its rapid growth and virulence at 20°C.