The prevalence of the methicillin-resistant Staphylococcus aureus (MRSA) among conventional pig herds in the Netherlands is high (around 71%). Nevertheless, information about the prevalence of MRSA among organic pig herds is lacking. Here, we report a study on 24 of the 49 organic pig herds in the Netherlands. The prevalence of MRSA positive herds showed to be 21%. The genetic characteristics of the MRSA isolates were similar to MRSA CC398 described in conventional pigs except one exceptional HA-MRSA CC30 found in one herd, which was presumably caused by human to animal transmission. This resulted in a prevalence of MRSA CC398 in the organic herds of 16.7%.