Staphylococcus aureus (S. aureus) is often the cause of mastitis problems in dairy herds and causes great economic losses. In this study, isolates from a dairy herd with a known S. aureus mastitis problem were examined by means of molecular methods (spa typing, PFGE, and DNA microarray) to investigate their epidemiological relationship and the success of intervention measures. The investigated dairy farm has a herd size of 60 cows and uses a fully automated milking system for milk production. A S. aureus strain, which contaminated the automated milking system and was subsequently spread among the herd through the latter, was suspected to be the origin of the mastitis problem within the herd. Thanks to the applied molecular methods, the common origin of the S. aureus isolates from the collected milk and swab samples could be shown. By culling chronically infected cows, optimising dry cow management and ensuring reliable intermediate cluster disinfection, the bulk milk somatic cell count improved.