In order to investigate the hydrolysis capacity of Lactobacillus helveticuson casein and the discrepancy of the peptides in the fermented products， the consumption the two major caseins， peptide dynamic change and peptidomics were studied， as well as the hydrolysis genes of the two Lactobacillus helveticus strains and the cell-envelope protease activity during fermentation. The results showed that the hydrolysis of β-casein and αs1-casein by the two Lactobacillus helveticus strains was significantly different with no obvious preference. The total contents of peptides increased initially during fermentation. The peptides with molecular weights of 2 000-10 000 u showed similar trends， while the peptides with molecular weights of 180-500 ugradually accumulated in the late stage of fermentation. The analysis by LC-MS/MS indicated that the peptides showed heterogeneity after 24 h of fermentation， with 7M3 generating more specific peptides， mostly from the f78-99 region of β-casein from the C-terminus of αs1-casein， whereas M108 produced more peptides derived from the N-terminal and intermediate sequences of αs1-casein. The two strains displayed different single cell-envelope proteinase gene and transport systems. The higher enzyme activity of M108 in the early stage of fermentation was observed.