| Summary: | The potential probiotic benefits of <i>Lactobacillus mucosae</i> have received increasing attention. To investigate the genetic diversity of <i>L. mucosae</i>, comparative genomic analyses of 93 strains isolated from different niches (human and animal gut, human vagina, etc.) and eight strains of published genomes were conducted. The results showed that the core genome of <i>L. mucosae</i> mainly encoded translation and transcription, amino acid biosynthesis, sugar metabolism, and defense function while the pan-genomic curve tended to be close. The genetic diversity of <i>L. mucosae</i> mainly reflected in carbohydrate metabolism and immune/competitive-related factors, such as exopolysaccharide (EPS), enterolysin A, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. It was worth noting that this research firstly predicted the complete EPS operon shared among <i>L. mucosae</i>. Additionally, the type IIIA CRISPR-Cas system was discovered in <i>L. mucosae</i> for the first time. This work provided new ideas for the study of this species.
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