Objective: to determine the frequency of the mecA gene in methicillin-resistant Staphylococcus aureus (MRSA) isolated from patients treated at a third-level hospital in the Cajamarca region, Peru; as well as, to determine which of the two antibiotics used as phenotypic screening is more useful in explaining the presence of said gene. Methods: 71 bacterial isolates were analyzed from samples obtained from the Hospital Regional Docente of Cajamarca. The identification of S. aureus was carried out using the MicroScan system. Phenotypic screening for resistance to methicillin was performed using the diffusion technique with cefoxitin and oxacillin discs. DNA extraction was performed by heat shock, mecA gene detection was performed through polymerase chain reaction. For data analysis, the statistical software SPSS v.25 was used. Results: from 71 isolates, 40 (56,3%) were MRSA carriers of the mecA gene, the majority of these isolates corresponded to hospitalized patients 22 (31,0%), being more frequent in bronchial secretion samples 27 (38,0%). Phenotypic screening with cefoxitin disc was a better predictor for the presence of the mecA gene [P=0,010; Exp(B)= 12,3] compared to the oxacillin disc. Conclusions: It is shown a high frequency of positive MRSA mecA in samples of clinical origin, mainly from hospitalized patients. It is important to establish surveillance guidelines to identify MRSA in all hospitals in the region.