Species of the genus Beauveria are entomopathogenic fungi used in biological control to protect against insect pests. Identification of species is based on observation of morphological, phylogenetic and genetic differences. Currently, MALDI-TOF (Matrix Assisted Laser Desorption/Ionization- Time of Flight) mass spectrometry is often used in microbial diagnostic but identification of Beauveria species has not been tested before. The aim of this work was the possibilities of this method and to compare it with genetic analysis. Twenty strains of B. bassiana and B. pseudobassiana isolated from insect cadavers, mycoinsecticides and soil samples were used. Sequences of ITS (Internal Transcribed Spacer) region were used for genetic identification of strains. Sequences and results from protein analysis of isolates were compared with the reference strains of B. bassiana and B. pseudobassiana. Results of MALDI Biotyper softvare identification were correct for all strains. Identification was reliable with high log score (>2.1) for most of strains. Score value less than 1 was observed only in a single case - strain GHA isolated from mycoinsecticide Botanigard.The result of both analyses was also dendrogram (phylogenetic tree) which showed high degree of result consistence. MALDI-TOF identification of fungi from Beauveria genus is usable for fast and reliable identification of entomopathogenic fungi isolates acquired from environment and results can be utilized in conservation biocontrol strategies in agriculture and forest ecosystems.