Ninety six consecutive, non-duplicate S. aureus isolates from clinical specimens were collected between January to December 2007 from six tertiary hospitals in Northeastern Nigeria analysed by phenotypic and molecular methods. Of the 96 S. aureus isolates, 12 (12.5%) MRSA isolates were identified by disc diffusion and confirmed by PCR assay, recovered from 2 of the 6 hospital (11 from UMTH and I from Gombe). Twelve MRSA and 4MSSA isolates exhibited multiresistant pattern to the commonly used antibiotics and 3 of the 12 MRSA were sensitive to clindamycin while all the S. aureus (MRSA and MSSA) isolates were susceptible to vancomycin, mupirocin and fusidic acid. Overall antibiotic susceptibility pattern demonstrated high level resistance with penicillin (92.1%), moderate level with gentamicin (14.6%), erythromycin (15.6%), cotrimoxazole (19.8%), ciprofloxacin (15.6) while low-level with clindamycin (9.4%) and rifapicin (2.1%). The SCCmec typing of the MRSA isolates by two standard typing methods revealed presence of novel SCCmec element that have not be documented in literature. The MRSA prevalence of 12.5% may be considered to be high in an environment without previous surveillance studies. The multiresistant pattern of the pathogens to frontline antibiotics posed serious public health problem because of cost and unavailability of alternate chemothrauptic option like vancomycin. The definition of SCCmec types affirmed divergent element of staphylococcal flora.