The genus Enterococcus involves bacteria that are part of the natural microbiota of the gastrointestinal tract of animals and humans and is also found in water, soil and food. In the food industry, is used as starter or probiotic cultures, developing sensory characteristics and contributing to the balance of the intestinal microbiota. It should be noted that E. faecium can be considered probiotic or pathogenic, depending on the strain. The aim of this study was to select and identify potentially bacteriocin-producing lactic acid bacteria in raw milk from naturalized Brazilian breeds Curraleiro Pé-Duro and Pantaneiro after a selective growth on MRS medium. Raw milk samples were aseptically collected from Brazilian breeds Curraleiro and Pantaneiro (10 animals each) and aliquots were submitted to a selective growth using MRS broth at 37°C/16 h. The broth was centrifuged twice to obtain a cellular concentrate for performing molecular analysis. LAB was determined through DNA extraction from milk, the 16S rRNA gene was amplified by PCR and optimized by Illumina TruSeq platform and analyzed with QIIME. A total of 42,899 sequences was formed. The only genus identified was Enterococcus, with higher frequency of E. faecium (86.18% of sequences) on 90% of the samples. Others species identified were E. mundtii (90% of samples and 9.34% of sequences), E. faecalis (10% of samples, 3.47% of sequences), E. lactis (90% of samples, 0.84% of sequences), E. durans (45% of samples, 0.11% of sequences), and E. hirae (15% of samples, 0.05% of sequences). Our hypothesis is that lactic acid bacteria naturally present in milk of these breeds have the ability to produce inhibitory compounds against pathogens, because these animals present low mastitis incidence and produce milk with low SCC, despite the absence of management to control mastitis. These compounds could be organic acids or bacteriocins and some strains of the identified species, such as E. faecium, are bacteriocins producers. Therefore, these microorganisms have technological potential for isolation and using in dairy products and affect animal health and food safety.