HA-MRSA cases/100 admissions increased from 1.36 (2000) to 2.00 (2006) and declined to 0.79 (2012). Overall, 9717 MRSA isolates underwent SCCmec genotyping. SCCmecI, the predominant cassette during the study period, peaked at 88% in 2003 and declined to 64% in 2012. SCCmecIV increased modestly from 10% to 16%, followed by SCCmecII with a strong increasing trend from 2% to 14%. Other types were minor contributors (SCCmecV, 3.4%; others <2%). Patients harboring SCCmecI and SCCmecII were older (median age, 76 and 82 y) compared to those with SCCmecIV (60 y). Strain distribution differed by hospital sectors. While SCCmecI remained the prevalent subtype in acute care (AC) and non-AC settings, the proportion of MRSA containing SCCmecII and SCCmecIV was higher in non-AC settings. SCCmecII increased from 6% to 32% in geriatrics. Genotyping confirmed ST228 South German-SCCmecI as the predominant clone. ST105 (CC5) appears to be the predominant clone of SCCmecII. Individual SCCmec replacement was observed in 123 patients (incl. 37 within SCCmecI-SCCmecII and 69, SCCmecI-SCCmecIV).