Insect killing fungus Beauveria bassiana has been widely studied as a biological control agent. However, many studies have been focused on lab or field-based management. Herein this work, comparison of three B. bassiana strains was investigated under a molecular level. The whole genome sequences of ERL836, JEF-007 were analyzed by PacBio (35.5 Mb of ERL836 and 36.5 Mb of JEF-007) and ARSEF2860 referenced from GenBank (33.7 Mb). To compare the three strains, virulence, thermotolerance and chemical resistance were assayed. The transcriptomes of non-infecting B. bassiana and infecting B. bassiana against western flower thrips were analyzed using RNA-seq. This work can provide that genome features, functions, morphology and gene expression could be different under the molecular level, even if in the same species.