The health effects of probiotics are strain-specific， making precise strain-level identification a core prerequisite for scientific research and the standardized development of the industry. This article， based on a review of domestic and international standards， regulations， and regulatory requirements， systematically expounds on the hierarchical technical pathways from phenotypic identification， molecular typing identification to whole-genome sequencing (WGS)-based identification， after clarifying the taxonomic principles of probiotics and the definitions of genus， species， and strain. Among them， WGS can provide high-resolution genomic information and has become the internationally recognized ‘gold standard’ for strain identification. The average nucleotide identity (ANI) analysis， core genome multi-locus sequence typing (cgMLST)， and single nucleotide polymorphism (SNP) analysis are the key technical means and parameters for achieving precise identification. Given the differences in evolutionary rates and genomic stability among different species， the determination of strain consistency should establish a SNP threshold system differentiated by species and genus， and conduct a comprehensive assessment in combination with insertion and deletion (InDel) features. In the future， probiotic strain identification technology will develop towards a diversified system of ‘scenario adaptation’， constructing a ‘molecular ID card’ for strains based on WGS data and integrating cutting-edge technologies such as artificial intelligence， providing solid support for scientific regulation， and industrial innovation in the probiotic industry.