Potato ( Solanum tuberosum L.) is one of the important food crops in the world. Early blight caused by Alternaria highly influences potato production annually. It has become an important disease of potato growing region of Iran , especially Isfahan province. During (2006-2007) 320 samples of infected leaves has been collected from potato fields of Isfahan , Ardebil , Khozestan, Hamedan, Semnan, Khorasan razavi provinces and tomato fields of Isfahan province. Based on morphological studies 247 fungal isolates were belonged to Alternaria ., 35 isolates to Ulocladium ., 27 isolates to Stemphylium . and 19 isolates to Drechslera . Seven Alternaria species i.e.; A. alternata, A. tenuissima, A. solani, A. arborescens, A. infectoria, A. dumosa and A. interrupta has been identified. Two species A. alternata and A. tenuissima were most prevalent. In order to study inter and intra species genetic diversity among isolates, IGS region amplified by using specific IGS primers. In case of A. tenuissima using IGS26 and 26S3111F primers complete IGS1, IGS2, end part of 28S and initial part of 18S as long as 2732 pair base has been amplified and sequenced. Molecular characteristics of Alternaria species were determined using PCR-RFLP analysis of intergenic spacer region with Alu I , Hin fI , Msp I and Rsa I enzymes. Morphological different isolates Ma4 and Ie1 belong to A. alternata and A. tenuissima separates from other species with high similarity coefficient based on molecular characteristics. This indicated that these two species are more similar despite morphological differences and growing pattern. There was no difference in disease severity and incubation period. Among species two isolates Se9 and Ie10 of A. dumosa and A. interrupta were more similar to each other. Isolate of A. infectoria belong to A. infectoria species-group which separated in different clade from others. In pathogenicity test isolates belong to this species was different by producing of yellow halo symptoms. Isolate of A. solani had major difference with other species; this specie is belong to large spore Alternaria and during pathogenicity test has a long common duration interval. Use of IGS sequencing that is longer than ITS sequencing may be more useful in genetic diversity study of Alternaria species.
