Insertion sequence (IS) elements were found to be associated with the truncation of predicted cellobiose transport, acetaldehyde dehydrogenase and diacetyl reductase genes in the genome of Lactobacillus helveticus DPC 4571. The conservation of the IS elements in these different genomic locations among L. helveticus cheese isolates was determined by amplification with gene-specific and IS element-specific primers. The presence of two of the IS elements was found to follow a genotypic profile of the strains generated by randomly amplified polymorphic DNA (RAPD)-PCR and strains that clustered by RAPD-PCR tended to have the IS element in the same position. However, the IS element that interrupted the cellobiose transport gene was found to be common to all strains tested. This conserved genotype suggests the insertion event occurred early in the evolution of L. helveticus as a separate species.