Naturally occurring fungal pathogens of stored-grain insect pests were identified and quantified using different insect sampling techniques in wheat and maize storage facilities in Central and South Anatolia in Turkey. Storage facilities were sampled by probing, trapping and visual inspection in five cities (Sanliurfa, Kahramanmaras, Adana, Mersin and Konya) from June to November 2013. Entomopathogenic fungi recovered from dead insects were identified to species level by sequencing the ITS1-5.8S-ITS2 region of the genomic DNA. Of the three species isolated, the majority were Beauveria bassiana (97 isolates), followed by Purpureocillium lilacinum (20 isolates). The third species, Beauveria varroae (9 isolates), is the first record on stored-product pest insects. Thirty-five isolates were from Tribolium spp., 29 from Sitophilus spp., 24 from Cryptolestes ferrugineus, 22 from Rhyzopertha dominica, 8 from Oryzaephilus surinamensis, 4 from Trogoderma granarium, 3 from Latheticus oryzae and 1 from a species of Cryptophagidae. The fungal infection of stored-grain pests did not vary significantly according to the time of sampling. A higher frequency of occurrence was recorded for Adana than the other cities and for Tribolium species than the other hosts. Grain samples taken by probing resulted in a higher frequency of fungal infection, but commodity type did not have a significant effect. The results demonstrated that (1) entomopathogenic fungi occurred at a low frequency, and (2) location, together with sampling technique, can affect their recovery. Further exploration of this ecosystem could yield important information for improving their use for management of stored-grain pests.