The present invention relates to unique agr gene sequences and primer sets for identifying CA-MRSA MW2 or CA-MRSA USA300 strains in clinical samples from various sources. More specifically, this invention provides fluorescent labeled primers which are designed to amplify 1) two unique agr gene sequences from each strain, 2) a partial spa gene and 3) a partial pvl gene. These primer sets can be packaged into one multiplex PCR kit for identifying MRSA strains that are most virulent and pathogenic.