Milk is an excellent medium for the growth of several bacteria and other microorganisms and thus, it has been extensively studied. An always current issue in the dairy industry is mastitis, which causes losses in milk volume and profits. In many cases, milk is used raw or treated at low temperatures for further dairy processes while there are quite a few cases in which foodborne-related outbreaks have occurred. Both culture-based methods and PCR were used to assess the presence of certain pathogens related to both contagious and environmental pathogens, especially the emerging pathogenic bacterium Klebsiella pneumoniae, as well as Staphyloccocus aureus and Enterobacter spp., which are associated with mastitis in milk samples from different lactating ruminant species (cows, goats, and sheep) and to further evaluate the significance of the isolated pathogens to public health. Even though significant mastitis contagious pathogens such as Staphylococcus aureus and Staphylococcus epidermidis were not detected, environmental pathogens related to poor hygiene conditions at the farm level (K. pneumoniae, Staphylococcus saprophyticus, and Enterococcus spp.) were detected. In particular, K. pneumoniae and Staphylococcus saprophyticus were present in ovine milk samples while bovine and caprine milk samples were contaminated with Enterococcus spp. The presence of these bacteria underlines the significant role of environmental hygiene especially since Staphylococcus saprophyticus and Enterococcus spp. are related to urinary tract infections and all of the tested pathogens may carry antibiotic resistance genes. More specifically, 20% of the isolated Klebsiella pneumoniae strains were found resistant to carbapenem antibiotics. The presence of emerging K. pneumoniae in ovine milk samples also indicates the need for new policies in terms of safety testing. Suggestions of monitoring processes carried out by the relevant authorities are discussed.