Milk samples of ewes’ and goats’ unprocessed milk were collected from milk tanks from various farms in Epirus, Greece and classified in two groups according to the type of farming. Analyses of the samples included microbial inhibition assays to detect the presence of antibiotic residues, isolation of Staphylococcus aureus and Escherichia coli strains as microbiological indicators for susceptibility to antimicrobial medicines, Somatic Cells and Coagulase Negative Staphylococci (CNS) counts. These findings were correlated with each other as well as to the stage of the lactation period and to the type of the farming practices. Monitoring of bulk tank milk for residues of antibiotics should be performed after heating of the milk, on a regular basis, and should include at least two different tests. The results point out that the type of farming affects the CNS counts as well as the prevalence of residues in the milk. Furthermore, the inverse correlation between CNS counts and prevalence of residues of antibiotics suggests a possible protective role of CNS. Resistance of the bacterial indicators to antibiotics was random and relatively rare, perhaps acquired in past due to misuse of antibiotics, turning the indicator microorganisms to reservoir of resistance.