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Bee bread is fermented and naturally preserved pollen that is enriched with digestive enzymes and organic acids from both honey and the salivary gland secretions of honeybees. As yet, there is insufficient information concerning which bacteria and yeasts are involved in the fermentation. This study seeks to determine the contents of microorganisms in fresh and dry bee bread samples and to ascertain the antimicrobial resistance of these isolated microorganisms. Fresh and dry bee bread samples were obtained from 8 different colonies that were cultivated in suitable medium to reproduction the aerobic microorganisms, anaerobic microorganisms, and fungi. The isolated strains in bee bread samples were identified by conventional and MALDI-TOF MS methods. The minimal inhibitory concentrations (MIC) of the antimicrobial agents for strains were determined according to the Clinical and Laboratory Standards Institute (CLSI). The 34 strains were isolated from fresh bee bread samples. There were no microrganisms reproduced in the dried bee bread samples. The 34 isolated strains were; Aspergillus spp. (12), Rhizopus oryzae (6), Mucor circinelloides (1), Bipolaris (2), Trichoderma (3), Paecilomyces variotii (1), Penicillium chrysogenum (1), Kodamaea ohmeri (1), Bacillus altitudinis/pumilus (3), Bacillus licheniformis (1), B. megaterium (1), Micrococcus luteus (1) and Serratia marcescens (1). The MIC values of itraconazole (IT), voriconazole, anidulafungin (AND), and caspofungin (CS) for Mucor and Rhizopus strains were higher (≥32 μg/mL), with the exception of amphamphotericin B posaconazole. All antifungal agents had lower MIC values compared to the Aspergillus, Bipolaris, P. variotii, and K. ohmeri strains. The trichoderma strains had low MIC values (≤0.50 μg/mL), with the exception of IT. The P. chrysogenum strains were found to have low MIC value (≤0.25 μg/mL) compared to posaconazole, AND, and CS. In this study, there were no microorganisms reproduce in the dried bee bread samples stored under suitable conditions. In addition, it was concluded that yeast, mold, and bacteria isolated in fresh bee bread samples may be resistant to antibiotics and antifungal drugs.