Methicillin-resistant Staphylococcus aureus (MRSA) have been described repeatedly in dairy herds. In this study, we compared the prevalence and antimicrobial resistance of MRSA in bulk tank milk from conventional and organic dairy herds in Germany. Samples were collected from 372 conventional and 303 organic dairy herds throughout Germany. Bulk tank milk (25 mL) was tested for MRSA using an established double selective enrichment method. The MRSA isolates were typed using spa typing and tested for resistance to 19 antimicrobials using the broth microdilution method. Methicillin-resistant Staph. aureus was detected more frequently in bulk tank milk from conventional (9.7%) than from organic (1.7%) dairy herds. Herd size and region were associated with differences in prevalence. Most isolates (38/41) were from spa types associated with the livestock-associated clonal complex CC398. Isolates from conventional herds tended to be more resistant to antimicrobials; however, because of the limited number of isolates from organic herds, no statistical tests were performed. In conclusion, prevalence of MRSA in dairy herds in Germany seems to be increasing and is more prevalent in regions with high livestock density. Organic herds are also affected although at a lower level. Therefore, MRSA should be specifically included in biosecurity protocols for dairy herds, and effective control measures need to be investigated.