Microorganisms such as Staphylococcus spp., in particular coagulase-positive strains, continue to pose a serious challenge to human and veterinary medicine. These bacteria can be a component of the natural biota of the body but can also cause infections in companion animals, including dogs and cats. Therefore, the aim of this study was to analyze the occurrence of Staphylococcus bacteria in companion animals, with particular emphasis on predilection sites, and to characterize these strains in the context of their epidemiological significance and threat to human health. Results We demonstrated that the dominant species were S. aureus and S. pseudintermedius, isolated primarily from the skin and oral mucosa of dogs. The most frequently tested strains were phenotypically resistant to penicillin, tetracycline, clindamycin, and erythromycin (80.2%, 64.4%; 62.4% and 59.4% respectively), while phenotypic resistance to methicillin was showed in 15 S. aureus and 42 S. pseudintermedius strains (56.4%). However, ultimately, 39 strains originating solely from dogs (22,2%) were classified as methicillin-resistant based on presence of mecA gene. Multidrug resistance was confirmed for 69.3% of the strains. Detailed characterization of the MRSA and MRSP strains revealed resistance or intermediate susceptibility to vancomycin for six and 12 strains, respectively. Since, more than one strain was present in the same dog, VIS and VRS strains were isolated from 11 of the 90 dogs tested (12%).The dominant sequence types in MRSP were the expansive, multidrug-resistant clone ST551, while ST398 was the dominant one in S. aureus, which colonizes livestock and occasionally causes infections in these animals as well as companion animals. Conclusion Our studies have confirmed that clinically healthy dogs are a significant reservoir of multidrug-resistant and potentially virulent strains of S. aureus and S. pseudintermedius. Our research also confirmed that the same animal can harbor several strains belonging to the same species, differing in resistance and virulence. We also confirmed the increasing prevalence of methicillin- and vancomycin-resistant strains in the microbiota of the skin and mucous membranes of healthy dogs. In summary, our results confirm that companion animals are a relevant reservoir of Staphylococcus spp., including coagulase-positive Staphylococcus strains, which are resistant to multiple antimicrobials. Therefore, protocols for the use of antimicrobials in companion animals should be very critically reviewed, as they can be a crucial link in the chain of spread of MRSA and MRSP strains.