Objective: To investigate the genomic differences of different phenotypic colonies of Lacticaseibacillus paracasei PC-01 after high-density fermentation. Methods: Ten L. paracasei PC-01 isolates with different phenotypic characteristics after high-density fermentation were subjected to whole-genome sequencing using second-generation sequencing technology， and the differences between these ten L. paracasei isolates were revealed by comparative genomics methods. Results: The genome size of the 10 L. paracasei PC-01 isolates ranged from 2.69 to 2.83 Mb， the GC content ranged from 46.50% to 46.64%， and the number of CDs ranged from 2 793 to 3 406， with small differences in genome size and GC content among the different colonies. The results of functional annotation showed that the number and types of genes encoding carbohydrate and protein metabolism， as well as genes involved in the synthesis and degradation of amino acids and their derivatives varied among different strains. Phylogenetic trees were constructed based on the core genes， and it was found that strains with similar colony morphology were located in the same branch. SNPs showed that every two isolates with the same colony morphology had the same mutation site， which further confirmed the association between colony morphology and genotype. Analysis revealed non-synonymous mutations in genes related to glycosyltransferases (epsJ， pbpF， ponA， etc.) and the ABC protein family (yheS， bceB， bceA， pcrA and uvrA， etc.) in all 10 isolates， allowing the strains to better adapt to their environment and thus survive the high density fermentation process. Colonies PC-01-3 and PC-01-4 differed markedly from other colony morphologies with non-synonymous mutations in the ltaS gene. The deficiency of lipophosphatidic acid synthase(LtaS) caused the bacteria to exhibit impaired cell division and growth defects， which may be the main cause of the differences in colony morphology. Conclusion: In this study， 10 isolates of L. paracasei PC-01 were analyzed at the genome-wide level， and the differences between colonies of the same strain were resolved to provide data for the follow-up study of L. paracasei PC-01.