The goal of this study was to delineate the molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) in Taiwan. Ninety-six MRSA isolates were collected from the blood cultures of different patients during the period July to December of 2008. The spa typing, staphylococcal chromosomal cassette (SCCmec) typing, mec-associated direct repeat unit (dru) copy numbers, and toxin genes (sea, seb, sec, tst, lukS/F) of each isolate were determined. Thirty-eight, 28, 18, and 12 MRSA isolates were SCCmec type II, SCCmec type III, SCCmec type IV, and SCCmec type V, respectively. Most (31/38, 81.6%) of the SCCmec type II isolates were of spa t002 with four dru repeats. Some of them also carried the sec or tst toxin gene (67.7 and 80.6%, respectively). Of the 28 SCCmec type III MRSA isolates, 15 (53.6%) were of t037 with 14 dru repeats, and all also carried the sea gene. Of the 18 SCCmec type IV MRSA isolates, 13 (72.2%) were of t437 with nine dru repeats, and ten of them also had the seb gene. Among the SCCmec type V MRSA isolates, nine were type V(T). Five (55.6%) of them were of t437 with 11 dru repeats, and all contained the lukS/F gene. The clonal spreading of SCCmec MRSA strains with specific spa and dru types was found. Further longitudinal, multiple-site surveillance is required in order to define the MRSA evolution in Taiwan.