Previous research on the identification of fungi by means of their Raman spectra (i.e. spectra based on the inelastic scattering of light) of their spores indicates that this approach could be a fast, cheap and reliable method to distinguish fungi. Entomopathogenic fungi are used in commercially available insecticides (mycoinsecticides), in particular species of the genera Beauveria and Metarhizium. The identification of fungi in infected organisms is necessary for efficacy studies as well as in environmental impact assessments. This study aims at developing a method to differentiate isolates of these fungi, more precisely isolates of Metarhizium brunneum (Ca8II, Cb15III, Cb16III), Metarhizium pemphigi (X1c) and Beauveria bassiana (DSM 62075) as a non-related reference. To this end, fungi were grown on different culture media (both artificial and natural); samples were taken at different ages of the culture to assess possible impacts of nutrition and age on conidial pigmentation. It was possible to obtain spectra from the conidia of these fungi. The final predictive model was capable of determining isolated conidia grown on model insects with an overall goodness of prediction of 98.8% without any further sample preparation. In conclusion, Raman microspectroscopy proves to be a reliable and fast approach to distinguish entomopathogenic fungi.