A total of 25 isolates of Alternaria sp.from different localities and host plants were amplified with 6 RAPD primers selected from 50 primers.69 RAPD markers were obtained,62 of them were varied.89.86% of them were polymorphic.The genetic distance and phylogenetic tree were constructed by use of PopGen32.Isolates were divided into 7 groups.The results showed that genetic divergence of all strains were closely related to their host plants and localities.