A total of 142 soil samples was collected from different Mexican states: Campeche (13), Michoacán (15), Nuevo León (25), San Luis Potosí (25), Sinaloa (17), Sonora (17), Tabasco (5), Tamaulipas (20), and Yucatán (5). Larvae of the greater wax moth, Galleria mellonella (L.), were used as bait to detect, trap, and multiply entomopathogenic fungi in vivo. Twenty-three percent of the soil samples processed were positive for the presence of entomopathogenic fungi according to the macroscopic and microscopic characteristics: Beauveria bassiana (Bals.-Criv.) Vuill. was detected in 12% (17 isolates), Metarhizium anisopliae (Metchnikoff) Sorokin in 1% (2 isolates), and Isaria fumosorosea (Wize) in 10% (14 isolates). Genetic variability of the fungi was analyzed using the sequences of internal transcribed ribosomal genes (ITS-5.8S-ITS2) and digested with the enzyme Haelll. PCR results generated fragments of 600 bp for B. bassiana and M. anisopliae, and more than 600 bp for I. fumosorosea. Both reference strains and field isolates produced similar restriction patterns. Genera of native entomopathogenic fungi were found in the diverse citrus areas of Mexico, opening the possibility for biological control of pests affecting citrus in each region.