Abstarct: Entomopathogenic fungi often in nature make insects diseases and important agent regulator insects population that nature of human had put it .Insect pathogenic fungus, Beauveria bassiana a famous as pathogens because of the wide host range as a biological pesticide is considered. This fungus wide range of hosts that least 10 orders and 40 families of insects are included, infects. In this research, to study genetic diversity this fungus, from different regions of ahvaz (khuzestan province) and shahrood (semnan province) 50 different isolates of B. bassiana fungus by Galleria Bait Method (GBM) have been isolated and using morphological traits such as growth rate, sporulation and germination power and pathogenicity against Tribolium castaneum (Coleoptera: Tenebrionidae) were described. Morphological experiments results revealed that among the parameters of growth rate, sporulation and percent pathogenicity there is a significant correlation. Also, in this research from replicated polymorphisms of micro-satellite ISSR markers to assess the levels of genetic diversity in 26 different isolates of B. bassiana fungus isolated from different geographic regions were used. In this study, from 30 primers evaluated, 24 primers on the basis of bond formation rate, polymorphism and repeatability of bands were selected. Mentioned 24 primers, in total 913 bands were produced, that all showed acceptable polymorphism. The number of replicated fragments by different primers were varied. The highest number of amplified fragment was 50 belong to ISSR840 primers and the lowest of them was 29 belong to ISSRBIS29 primers. The highest Shannon's variation coefficient, Nei's variation coefficient, Effective number of alleles, Polymorphism Information Content and Marker Index belong to ISSR840 primers that indicates that this primers variation between isolates show better. The results of this research indicate a molecular and morphological diversity among isolates and showed the efficiency of ISSR markers for determine genetically diversity of between different isolates that were studied.