Since the health benefits conferred by probiotics are strain-specific, identification at the strain level is essential to monitor the presence and abundance of specific probiotics in the product or GI tract. Compared with the standard plate counting method, PCR-based methods (standard PCR and quantitative PCR) can shorten the detection time and improve the specificity, which is well suited for the detection or quantification of probiotics. Known phenotypic or genotypic characteristics of target strains can also be used to develop strain-specific assays. However, the initial stages of strain-specific test development can be replaced by comparative genomic analysis of the target genome versus the relevant genome in public databases. Quantitative genomic DNA from probiotics or next-generation probiotics can be used for assay development and validation. The quantitative format also allows for use in quantitative research and analysis and laboratory quality control.