Lactobacillus helveticus is used for the manufacture of cheeses and milk-based products. Although it is not considered a probiotic microorganism, some strains demonstrated beneficial effects through the production of antihypertensive peptides from the hydrolysis of casein during milk fermentation. Strain-specificity of bioactive peptide production by L. helveticus makes the availability of reliable typing methods essential for both legal and good manufacturing processes. Accordingly, RAPD and inverse-PCR of five insertion sequence elements were comparatively evaluated for the molecular characterisation of four L. helveticus dairy cultures producing antihypertensive peptides and fourteen reference strains. Calculation of discriminatory indices and cluster analysis of the DNA fingerprints confirmed the suitability of both approaches for acceptable strain differentiation. Although RAPD was more discriminating, for a few test strains a neat discrimination was only achieved through multiplex inverse-PCR, thus suggesting the suitability of a combined analytical approach for a finer strain discrimination.