BackgroundThe mountain pine beetle,Dendroctonus ponderosae, is an irruptive bark beetle that causes extensive mortality to many pine species within the forests of western North America. Driven by climate change and wildfire suppression, a recent mountain pine beetle (MPB) outbreak has spread across more than 18 million hectares, including areas to the east of the Rocky Mountains that comprise populations and species of pines not previously affected. Despite its impacts, there are few tactics available to control MPB populations.Beauveria bassianais an entomopathogenic fungus used as a biological agent in agriculture and forestry and has potential as a management tactic for the mountain pine beetle population. This work investigates the phenotypic and genomic variation betweenB. bassianastrains to identify optimal strains against a specific insect.ResultsUsing comparative genome and transcriptome analyses of eightB. bassianaisolates, we have identified the genetic basis of virulence, which includes oosporein production. Genes unique to the more virulent strains included functions in biosynthesis of mycotoxins, membrane transporters, and transcription factors. Significant differential expression of genes related to virulence, transmembrane transport, and stress response was identified between the different strains, as well as up to nine-fold upregulation of genes involved in the biosynthesis of oosporein. Differential correlation analysis revealed transcription factors that may be involved in regulating oosporein production.ConclusionThis study provides a foundation for the selection and/or engineering of the most effective strain ofB. bassianafor the biological control of mountain pine beetle and other insect pests populations.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12864-023-09473-4.