The presence and distribution of genotypes from malolactic starter cultures between the autochthonous microbiota in fermenting Rioja wines have been studied in this paper. The commercial cultures characterization allowed to identify different species and common pulsed field gel electrophoresis and randomly amplified polymorphic DNA genotypes in several brands of Oenococcus oeni starter cultures. Four indistinguishable genotypes were found between the commercial and the autochthonous O. oeni strains. These four genotypes appeared during different vintages in seven of the 10 sampled wineries despite bacterial starter cultures had never been used. Therefore, the detection of commercial LAB genotypes indistinguishable from the autochthonous ones involved their removal from a selection process. These genotypes represented the 17.7% of autochthonous O. oeni isolated in this region during three consecutive years. This fact demonstrated that performing similar studies as previous selection criteria is advisable to avoid large work and the proposal of one commercialized bacteria. (c) 2014, The Society for Biotechnology, Japan. All rights reserved.