Methicillin resistant Staphylococcus aureus (MRSA) has been identified as an emerging pathogen in livestock animals that is readily transferable to humans in contact with livestock. Moreover, MRSA is a mastitis pathogen in dairy cows that can be isolated from bulk tank milk. It was the objective of this study to characterize MRSA from bulk tank milk with respect to their spa- and SCCmec-type, their phenotypic antimicrobial resistance and resistance resp. virulence associated genes using broth microdilution and a microarray for S. aureus. Bulk tank milk samples (25 ml) were tested for MRSA using a 2 step selective enrichment protocol. Presumptive MRSA were confirmed using a triplex PCR targeted at identification of S. aureus and the mecA gene that encodes resistance to methicillin. A total of 36 isolates derived from monitoring programs and collected within other frameworks in 2009 and 2010 were included in the characterization. All isolates displayed spa-types assigned to the clonal complex CC398. Based on the epidemiological cut-off values for the interpretation of minimum inhibitory concentrations isolates were resistant to tetracycline (100%), clindamycin (58%) erythromycin (52%), quinupristin/dalfopristin (36%) and kanamycin (27%). Isolates did not carry genes associated with typical virulence factors for S. aureus such as the Panton-Valentine Leukocidin. However they did carry hemolysin genes. Results show that livestock associated MRSA of clonal complex CC398 does occur in German dairy herds and that the strains have similar properties as described for strains from pigs.