Abstract: This study was carried out for twenty retail and bulk maize samples parallel for each group, surface disinfected and non-disinfected maize kernels, in Balikesir, Turkey. The aim of the study has provided information to compare species diversity between non-disinfected and disinfected maize mycoflora. Rhizopus (49%) and Aspergillus (19%) were the most frequent genera isolated in non-disinfected maize kernels. Three species of Rhizopus spp. were commonly isolated; R. oligosporus Saito (19.0%), R. oryzae Went and Prinsen Geerlings (8.1%) and R. stolonifer (Ehrenb.) Lind. (22.0%). Aspergillus was the second most frequent genus isolated from non-disinfected maize kernels. Predominant species isolated were Aspergillus tubingensis (Schöiber) Mosseray (4.6%) and A. niger Van Tieghem (23%). In the disinfected group, Aspergillus spp. (25%), Fusarium spp. (21%), Rhizopus spp. (21%) and Penicillium spp. (13%) were commonly isolated. Aspergillus tubingensis (5.0%), A. foetidus var. acidus Naka, Simo and Wat (5.0%), Fusarium proliferatum (Matsushima) Nirenberg (17.1%), Rhizopus oligosporus (57%) and Penicillium oxalicum Currie and Thom (7.6%) were most frequently species isolated. Decrease of the Rhizopus genus by chlorine disinfection caused significantly increase of the Fusarium (21%), Trichoderma (8%) and Aspergillus (25%) rates. Fusarium proliferatum was also found dominant and potential mycotoxigenic “storage fungi”? in the samples of corn maize.