Lactococcus lactis is the lactic acid bacteria most used in the manufacture of dairy products because of its fast lactose fermentation and flavor production. In this study. L. lactis strains isolated from different sources and previously characterized and evaluated for their capability to produce flavor were compared with respect to their phenotypic and genotypic characteristics. The variability of phenotypes and genotypes in the L. lactis strains were influenced by the source of isolation. In general, strains that shared the same genotype presented different phenotypes, and only some genotypes were clearly related to the source of isolation. On the other hand, phenotypic characteristics such as coagulant activity and utilization of lactose, glucose, and arginine were closely related to the ecosystem of origin. Coagulant activity and lactose utilization, phenotypic characteristics that are of utmost importance for efficient flavor production by starters in the manufacture of dairy products, were better for strains isolated from raw milk dairy products than for those isolated from vegetables.