The performance of Patagonian Lactobacillus plantarum and Oenococcus oeni strains as malolactic starter cultures was compared. Two autochthonous strains of each species were selected, based on the presence of aroma-related genes, and inoculated in sterile wine of high ethanol content. The effects of initial inoculum size and acclimation treatment on the efficiency of malolactic fermentation (MLF) were analyzed for each strain. O. oeni strains were able to successfully conduct the MLF only when the inoculum concentration was higher than 1.108 CFU/mL and cells were acclimated in sublethal ethanol concentrations. The increase of ethanol concentration in the acclimation medium also improved the kinetics of malic acid consumption. Successful MLF with L. plantarum strains required lower inocula and no acclimation treatment. In addition, these strains showed a better profile of aroma-related genes than O. oeni. L. plantarum strains appeared to be more efficient than O. oeni strains as candidates for malolactic starter cultures to be used in Patagonian red wines. •L. plantarum and O. oeni strains were isolated and fermentation examined.•L. plantarum was more efficient at MLF than O. oeni in Patagonian wines.•Standardization of acclimation and inoculum was necessary for successful MLF by O. oeni.•Acclimation in high ethanol content improved the malic acid consumption of O. oeni.•MLF with L. plantarum strains required lower inocula and no pre-acclimation treatment.