Tobacco is one of the major industrial crops cultivated worldwide. Chemical control is the main method employed to reduce damage by insect pests. The use of entomopathogenic fungi represents an alternative to replace insecticides. The search for effective strains in the field constitutes a first step when developing a formulation. The objective of this work was to study genetic differences among isolates of entomopathogenic fungi obtained from tobacco grown soils using ISSR markers. The pathogenicity of the strains towards Helicoverpa gelotopoeon and Diabrotica speciosa was also assessed in order to search for a relationship between virulence and genetic diversity. Nineteen isolates were identified according to morphological features and molecular techniques as Beauveria bassiana (11) and Purpureocillium lilacinum (8). The diversity tree generated by ISSR analysis showed a high diversity among the strains. The pathogenicity towards H. gelotopoeon and D. speciosa was assessed and the logistic models generated showed that B. bassiana isolates LPSc1215 and LPSc1364 were the most pathogenic against both insect pests tested. In the diversity tree, these strains were grouped in a same cluster with a similarity level of approximately 85%, indicating a possible relationship between virulence and the band pattern generated.