The purposes of this study were to identify differences in the phenotypic resistance to antimicrobials and in the spa-types between 273 methicillin-resistant Staphylococcus aureus (MRSA) isolates derived from conventional (n = 21) versus organic pig farms (n = 10) located in Germany. The susceptibility of the isolates against 19 antimicrobial agents was tested and then compared between the two different husbandry systems. A statistically significant difference was observed between the MRSA strains isolated on conventional and on organic pig farms for the antimicrobials tilmicosin (61.8% vs. 40.0%; OR: 2.42), clindamycin (63.5% vs. 45.7%; OR: 2.06), gentamicin (14.7% vs. 34.3%; OR: 0.33), apramycin (3.8% vs. 22.9%; OR: 0.13) and enrofloxacin (13.9% vs. 34.3%; OR: 0.31). Finally, the results of the susceptibility testing were analysed in order to determine the resistance pattern per isolate. Among the tested isolates a kind of"basic resistance pattern of MRSA"to penicillin, ampicillin and tetracycline was identified. The predominant spa-types in both groups were t011 and t034. Less frequently detected spa-types were t1430, t1197, t2510, t779, t1451 and t1250.