We identified a novel type-III staphylococcal cassette chromosome mec (SCCmec) element carried by eight methicillin-resistant Staphylococcus aureus (MRSA) strains from different wards and patients in an Indian hospital. Although the pulsed-field gel electrophoresis pattern and spa types of eight strains were identical and clonally related to other nosocomial Indian isolates that belonged to sequence type (ST) 239 and spa type t037, the minimum inhibitory concentration (MIC) of these eight variants was noticeably low compared with the typical type-III isolates from the same hospital, and we were unable to identify ccrC and hsdR by multiplex PCR, although mer operon and transposases A, B, and C of Tn554 were amplified. By amplifying the entire SCCmec region by long-range PCR and determining parts of the nucleotide sequences of one isolate (V14), we found that the strain carried a novel SCCmec element containing a 422 bp sequence, which is highly homologous to that identified in strain CCR1-9583, mer operon and plasmid pT181 integrated in tandem via IS431 in the J3 region. It also carried a cassette chromosome, previously reported to be an SCC-like element, downstream of type-III SCCmec. Because PCR amplification of representative genes showed that these eight strains carried the same genetic elements, they belong to a novel MRSA clone that differs from most nosocomial clones carrying type-III SCCmec and SCCmercury, despite belonging to the ST239 genotype.