Enterococci are a ubiquitous group and are natural constituents of the intestinal flora of nearly all animals and humans and can reach high levels in a variety of farmhouse cheeses. The purpose of this study was to determine the origin of the different enterococcal strains present in cheeses at different stages of ripening by typing the enterococci isolated from the raw milk, the cheeses, the cheesemaking environment, and from the faecal matter of the ewes and humans associated with cheese production. The potential presence of vancomycin-resistant enterococci (VRE) at all stages of the process and in the cheeses was also considered. The study was carried out at two separate cheesemaking dairy plants, and samples of the ewes' faeces, the shepherds' and cheesemakers' stools, teat cups, vat, brine, holding tank milk, vat milk, and the cheeses after brining and after 1, 15, and 60 days of ripening were collected. Cheesemaking procedures at the two plants were similar, yet the enterococcal levels and species observed differed at all the sample collection points, though E. faecalis predominated in all the milk and cheese samples. The traceability study performed for the species E. faecalis present at all the sample collection points suggested that the cheesemaker and the cheesemaking equipment were the source of the enterococci in the cheeses, though other possible non-faecal sources remain to be determined. VanC1 and vanC2/C3 enterococcal strains were isolated from the ovine faeces, teat cup, brine, and vat samples at cheesemaking dairy plant A, while only two vanC2/C3 strains were isolated from ovine faeces samples at dairy plant B. No VRE strains were detected in any of the milk or cheese samples.