The sugarcane aphid, Melanaphis sacchari, is a key pest that affects sorghum in Mexico. During 2014 to 2016, in South of Tamaulipas sites and Bajio region in Guanajuato, the populations of this aphid were infected by different species of Hypocrealean fungi. Based in the morphometric identification and molecular characterization, the species associated with sugarcane aphid in South of Tamaulipas were Lecanicillium longisporum, Beauveria bassiana and Isaria javanica. In this region, the higher infection levels were caused by L. longisporum, mortality range from 30.0% to 50.0%. The presence of I. javanica and B. bassiana represented less than 26.0% and 10.0%, respectively. In Guanajuato, the species found corresponded to L. longisporum and B. bassiana. The infection levels of both species in sugarcane aphid populations in Guanajuato sites were less than 1.00%. The natural occurrence of entomopathogenic fungi on sugarcane aphid populations was associated with climactic factors such as temperature and relative humidity and development of infections was possibly affected by abiotic factors such as crop phenological stage and applications of chemical insecticides realized by farmers for control of this aphid. Further studies on the ecology and physiology of these fungi and trials to determine virulence and persistence in M. sacchari populations are needed. This is the first report on natural presence of L. longisporum, B. bassiana and I. javanica causing disease on Melanaphis sacchari in Guanajuato and Tamaulipas, Mexico.