Apple is one of the most important economically fruit plants of the world. Alternaria mali (Alternaria alternata apple pathotype) causes huge loss by infecting leaves and fruits. It can infect upto 85% of leaves in highly infected orchards. The fungus causes leaf spots which enlarge in zonate, circular or cresent shaped rings. Understanding the genetic variability of the pathogen is very important for devising the strategies to control it. DNA based molecular markers have been successfully used for studying the genetic variation in different fungal pathogens. During present investigation sampleswere collected fromdifferent areas ofKashmir valley. For molecular characterization two molecular markers RAPD and ISSR were used for characterization. Clustering in dendrogram indicates that isolates fromall regions were intermixed.Also there were no cultivar specific isolates identified.