Staphylococcus aureus is recognized for causing contagious mastitis in cattle. Elimination of the organism in affected animals is challenging due to its potential antibiotic resistance mechanisms and virulence factors. The aim of the study was the pheno- and genotypic epidemiological characterization of S. aureus isolated from bulk tank milk samples obtained from three municipalities in the northern region of Antioquia. Twenty-one S. aureus isolates from 150 bulk tank milk samples were characterized by evaluating antimicrobial susceptibility to 17 antibiotics using the VITEK 2, and identifying several genes encoding for virulence factors, enterotoxins, and the agr groups by conventional PCR. The clonal relationship between the isolates was assessed using macrorestriction fragment analysis (MRFA) of chromosomal DNA by pulsed-field gel electrophoresis (PFGE). Most of the isolates showed susceptibility to the tested antibiotics; 19% exhibited resistance to tetracycline and all isolates showed beta-lactamases. Molecular typing revealed that 76% carried the agrI and cap5 genes. Seven isolates harbored genes coding for staphylococcal enterotoxins (SE), with seh being the most identified gene. Furthermore, MRFA demonstrated high heterogeneity among the isolates, resulting in the assignment of 18 different MRFA patterns. These results indicate phenotypic resistance to tetracycline and beta-lactams, the presence of genes encoding for staphylococcal enterotoxins, and high heterogeneity among S. aureus isolates from bulk tank milk.