Oenococcus oeni is the best adapted bacterium to the harsh wine medium. Its growth is necessary after the alcoholic fermentation for the improvement of wine during malolactic fermentation. Inspite of the low pH, ethanol concentration and several other bacterial inhibitors, such as free fatty acids and some phenolic acids, O. oeni actively grow in wine. The efficiency of different starter cultures often used during the winemaking process is related to their inherent ability to survive and multiply. Bacteria use sophisticated mechanisms to enable them to survive a variety of environmental stresses. Among the stress genes whose expression changes in response to various stimuli in Oenococcus oeni several have already been identified. The objective of the present study was to determine genetic markers which should be used for the selection of O. oeni strains. A comparative genomic analysis was carried out between two O. oeni strains with opposite oenological potential. By Polymerase Chain Reaction (PCR) we checked among 80 O. oeni strains the presence of 46 genomic sequences derived from the comparative genomic analysis. Statistical analysis revealed 11 possible genetics markers. Their expression was quantified by reverse transcription quantitative polymerase chain reaction (RT-qPCR), for 14 efficient O. oeni strains and 5 less adapted. The quantification of transcription levels of the 11 genetics markers after a heat shock, acid and ethanol stress, exponential and stationary phase was determined. According to the gene, their transcription levels increased or decreased greatly in stress conditions.