Objective: Lactobacillus(L.) helveticus is one of the important starters and widely used in cheese and fermented milk drink. This study aimed to analysis the genetic background and genomic differences of L. helveticus strains， taking L. helveticus H9 and H10 as example， which would lay the genetic foundation for the identification and development of L. helveticus strains. Method: Taking L. helveticus H9 and H10 as examples， combined with the complete genome of other 16 strains of L. helveticus in the NCBI database， the genetic differences between strains were explored by comparative genomic methods. Result: There were diversity in genome size and the number of plasmid， CDSs， tRNA and rRNA among different L. helveticus strains. Phylogenetic analysis showed that L.helveticus H9 and L. helveticus H10 clustered in different evolutionary branches， and the L. helveticus H9 has closer phylogenetic relationship with industrial starter strains L. helveticus CNRZ32 compared with L. helveticus H10. The average nucleotide identity(ANI) clustering result almost consistent with the phylogenetic tree. L. helveticus H9 and L. helveticus H10 were clustered in different groups and the genomic sequence consistency between fermented dairy product isolates were lower than homo-feces/gut isolates. Comparing with L. helveticus DPC4571， the genomic sequences of L. helveticus H9 and L. helveticus H10 both had certain fragments insertion， deletion and inversion. There were differences between the specific functional genes of L helveticus H9 and L. helveticus H10， which of L. helveticus H10 were more involved in amino acid and energy metabolism. Conclusion: Analysis of L. helveticus genome information by comparative genomic methods found genetic differences among different L. helveticus strains.