Honey samples obtained by beekeepers taken from thirty-five different apiaries in Turkey’s region of Marmara were investigated for the presence of microorganism. Each honey sample was examined for the number of total aerobic mesofilic bacteria, coliforms, moulds and yeasts and the presence of Salmonella spp., Clostridium botulinum, along with other aerobic bacteriae such as Paenibacillus larvae and Melissococcus plutonius. In total, fifty-four honey samples of different botanical origins including unifloral (Umbelliferae, Leguminosae, Trifolium, Onobrychis), multifloral and chestnut were evaluated in the means of microbiological properties. Microorganisms were isolated in twenty-eight samples (60.86%) of pure cultures and eighteen samples (39.13%) of mixed cultures. On the other hand, no microorganisms were isolated in eight samples. Bacillus spp, Corynebacterium spp., Streptococcus spp., Staphylococcus spp. C. albicans and Penicillium spp. were isolated and identified in other honey samples. The bacteria counts were 4×102 - 1.4×103 cfu/g for aerobic mesofilic bacteria and 1-185 cfu/g for the fungi. The application of sanitary practices (hand washing, avoidance of sneezing or coughing, etc.) may be effective in controlling contamination by microorganisms. On the other hand, air, equipment and dust may be contributing causes of microbiological contamination. Therefore it is important to take precautions in order to avoid such contamination, even though such factors are often difficult to control.