Food contamination, either from microbiological or chemical, is the highest concern for public health. The dairy products such as cheese have an essential role in human nutrition but have been linked with outbreaks of foodborne illness. The cheese production process contains the steps that might be the reasons of bacterial pathogens contamination. The primarily purpose of this study was to detect the microbiological quality and Lactic Acid flora of cheeses at retail sale in bazaars of Bayramic, Ezine and Kepez (towns of Canakkale) which were produced at home or small dairies. The presence of Total Mesophilic Aerobic Bacteria (TMAB), Total Psychrophilic Aerobic Bacteria (TPAB), yeast and moulds, coliform bacteria, coagulase positive Staphylococcus spp., and Escherichia coli O157:H7 (EHEC) were investigated. The mean TMAB counts were assessed as 3.63 × 108 cfu/g (2.00 × 106- ≥ 1.00 × 109 cfu/g), 2.19 × 108 cfu/g (1.00 × 104- ≥ 1.00 × 109 cfu/g), and 1.55 × 108 cfu/g (2.00 × 106- ≥ 1.00 × 109 cfu/g) in cheese samples from Bayramic, Ezine and Kepez, respectively. TPAB was not determinated. The mean counts of coliforms were determinated as 1.44 × 105 cfu/g (ND- ≥ 1.00 × 106 cfu/g), 1.04 × 105 cfu/g (ND- ≥ 8.00 × 105 cfu/g) and 5.71 × 101 cfu/g (ND- ≥ 8.00 × 102 cfu/g) in cheese samples from Bayramic, Ezine and Kepez respectively. E.coli 0157:H7 and coagulase positive Staphylococcus aureus were not detected. The average colony counts of Lactococcus spp., Enterococcus spp. and Lactobacillus spp. were detected as 2.07 × 108 cfu/g (ND- ≥ 1.00 × 109 cfu/g), 2.43 × 106 cfu/g (ND- ≥ 3.30 × 107 cfu/g) and 1.54 × 108 cfu/g (ND- ≥ 1.00 × 109 cfu/g) in town Bayramic; 1.86 × 108 cfu/g (ND-1.00 × 109 cfu/g), 1.46 × 105 cfu/g (ND-6.1 × 106 cfu/g) and 1.31 × 108 cfu/g (ND- ≥ 1.00 × 109 cfu/g) in town Ezine; 9.57 × 107 cfu/g (ND- ≥ 1.00 × 109 cfu/g), 1.23 × 105 cfu/g (ND-1.00 × 106 cfu/g) and 8.24 × 107 cfu/g (ND- ≥ 1.00 × 109 cfu/g) in town Kepez, respectively. According to this study results, cheese samples produced without uncontrolled conditions such as in small dairy farms or home and sold in bazaars of Canakkale have high microorganism loads and do not meet the microbiological criteria in Turkish Food Codex regulations.