AbstractLactobacillus plantarum is one of the most extensively studied Lactobacillus species because of its presence in a variety of environmental niches, versatility, and metabolic capabilities, resulting in the use of this organism in many industrial applications. However, although extensive effort has been invested in screening this species from a variety of habitats, a reliable and accurate method for studying the succession and ontogeny of this organism in complex ecosystems is still required to confirm the activity of L. plantarum at the subspecies level. Therefore, in this study, novel subspecies-specific genes for the quantitative detection of two L. plantarum subspecies were identified by comparative genomic analysis. The specificity of primer sets for selected genes specific to each targeted microbe was confirmed in kimchi samples. Interestingly, in all the kimchi samples at 4 °C, the presence of L. plantarum subsp. argentoratensis was not observed. Hence, we found that low temperatures markedly affected the ontogeny of L. plantarum subsp. argentoratensis during kimchi fermentation. Subsequently, this touchstone method will offer new insight and metrics to understand the ontogeny and succession of L. plantarum subsp. plantarum and L. plantarum subsp. argentoratensis in various niches.