Approximately 39 Italian cheeses carry protected designation of origin (PDO) status. These cheeses differ in their manufacturing technology and the microbial flora which comprise the finished products. The evolution of lactic microflora in cheeses with PDO status is of particular interest because the biochemical activities of these organisms participate in cheesemaking and may play an acknowledged role in the development of organoleptic characteristics during ripening. Nonstarter lactic acid bacteria (NSLAB) constitute complex microbial associations that are characterized by the occurrence of various species and many biotypes as a result of a number of selective conditions persisting during the manufacturing process and different ecological niches. The evolution of different species during ripening of Fiore Sardo showed that, when present, Lactobacillus paracasei persists and dominates the microflora of the cheese in the last period of ripening, suggesting that this species, more resistant to the constraints of the mature cheese, could be involved in proteolysis and in other enzymatic processes occurring during cheese ripening. In contrast, the stretching step typical of pasta filata cheese, such as Ragusano, induced a simplification of the raw milk profiles, allowing the persistence only of some predominant species, such as Streptococcus thermophilus, Lactobacillus delbrueckii subsp. lactis, Lactococcus lactis, and Streptococcus macedonicus, after the stretching step. Lactobacillus plantarum and L. paracasei were isolated from ripened Castelmagno PDO cheese samples with the highest frequencies. These species, generally absent in the milk, occur in dairy ecosystems and dominate the bacterial flora of many ripened semihard cheeses. In PDO long-ripened Italian cheese such as Parmigiano Reggiano, the NSLAB population is mainly formed by L. paracasei, Lactobacillus rhamnosus, and Pediococcus acidilactici. Lactobacillus helveticus, L. delbrueckii subsp. lactis, and L. delbrueckii subsp. bulgaricus were also detected. Continued insight into the microbial populations of traditional Italian cheeses will allow continued production of characteristic, high-quality cheeses which have been enjoyed for many centuries.