A random amplified polymorphic DNA (RAPD) assay coupled to a fast and reproducible cell lysis method from Lactobacillus colonies were developed to type lactobacilli of different strains and species, with the aim of precisely enumerating each of the different Lactobacillus strains inoculated in a nutrient-rich environment, such as sausage meat batter. Colonization assays were carried out in an aseptic meat fermentation system for up to 14 d and the inoculated strains were challenged with mixtures of wild lactobacilli. The proportion of inoculated strains remaining at different times was compared with the total number of lactobacilli grown on MRS agar by RAPD. The colonization rate of the different strains tested was very different. The RAPD-fast lysis method developed is simple and, with a low cost per assay, could also be applied to other food fermentations.