The aim of this study is to isolate and identify A. flavus and study the genetic diversity among these isolates by using RAPD. Eleven collected samples were characterized depending on its morphological state, then DNA was extracted from them. RAPD markers are randomly banding with sites of genome more than, markers, where the primer UBC 809achieved discriminative power (19.1) and 43 bands, while6 achieved discriminative power (17.1) with 32 bands. There were more efficiency in specific binding, then RAPD primers have great binding to produce unique band, when 9 primers from 10 primers, 9 produced (5) unique bands, while RAPD markers showed low ability to produce unique bands, 3primers from 9 primers were produced as unique bands. The dendrogram of RAPD was reverted than isolates number 5 and 7 which had the genetic diversity 0.33361, while the isolates number 5 and 6 had the lowest genetic similarity 0.98521 in contrast with markers which showed isolates number1 and 2 genetic diversity 0.97826 while the isolates number 5 and 7 had the lowest genetic similarity 0.10253.