Beauveria bassiana has been used for the control of agricultural pests. However, the genetic diversity of these fungi in the State of Sergipe, Brazil has been poorly studied. The objective of this study was to quantify the genetic diversity of B. bassiana isolates by means of RAPD markers, microsatellites, and rDNA-ITS regions, relating their origins and different geographic hosts. Nineteen primers were used in the RAPD analysis, and four primer pairs were used as microsatellite markers. The rDNA-ITS of 18S rDNA region were evaluated using primers ITS 1 and ITS 4. The RAPD analysis showed genetic similarities from 2% to 77%. Isolates 057.99 and 053.96 had the highest similarity (77%), followed by 064.99 and 053.96, with 73% similarity. With regard to microsatellites, isolates BC.05 and 032.91 showed the highest genetic similarity (82%), followed by 064.99 and 057.99 isolates, with 80% genetic similarity. The analysis of the rDNA-ITS region showed an intense fragment with 550pb for all isolates. PCR products were digested with EcoRI and HaeIII, but no restrictions were found for such products.