The strains MT and E9 of Metarhizium anisopliae were found to be effective in causing the morphological changes in pupae of Diatraea saccharalis of different ages. However, during the treatment with the two strains, it was observed that there was a decrease in the longevity of old pupae and adults that emerged from old and young pupae. The adults that emerged died 24 h later and were totally covered by the pathogen's mycelium. Regarding the mortality of pupae of different ages, but in relation to the abnormalities, the pre-pupae were found to be more susceptible. The morphological alterations observed in the cuticle and in the internal tissues of the pupae were analyzed using a stereomicroscope, a light microscope and a scanning electron microscope. The adhesion stage and formation of the appressorium happened 18 h after the infection, occasioning black spots and depressions in the cuticle of young and old pupae. In pre-pupae, the sclerotization was not observed and the fungus acted faster and more effectively, thereby, achieving 100% mortality. The colonization of the pathogen was observed in young pupae between 48 and 120 h. The alterations were observed in the fat body, digestive system and musculature; moreover, several vacuoles were noticed inside the pupae. The extrusion happened after 120 h, presenting the mycelial growth upon the pupae cuticle and further sporulation upon the corpses. The morphological alterations that took place during the development of M. anisopliae suggest the possible causes for the mortality of the pupae of D. saccharalis.