Lactococcus lactis is the most commonly used cheese starter, due to its fast growth in milk, rapid production of lactic acid, and crucial role in cheese flavor and texture development. These characteristics are often strain-dependent and can result in dramatically different cheese quality, depending on which L. lactis strains are present during fermentation and aging. Therefore, a rapid and inexpensive tool capable of strain-level identification of L. lactis would be of great value to the cheese industry. One potential option, which has been successfully used to differentiate Lactobacillus strains, is repetitive sequence-based PCR, followed by high-resolution melt analysis (rep-PCR/HRM). Our aim was to determine if rep-PCR/HRM is suitable for strain-level differentiation of L. lactis. Three sets of repetitive element primers (i.e., GTG5, BOXAIR, REP1R-I/REP2-I) were investigated for their ability to distinguish 14 laboratory strains and 8 industrial strains of Lactococcus lactis, using hierarchal cluster analysis. The discriminatory power of each primer set was determined as the proportion of correctly paired melt curves, generated from duplicate PCR reactions. While some primer sets performed better than others, no single set was able to correctly separate all 22 L. lactis strains. However, the discriminatory power was improved when considering strain-clustering patterns from 2 or more primers sets. This demonstrates that a multi-assay approach to rep-PCR/HRM may be useful for confirming L. lactis starter strain identity.