The skin microbiota interacts with the host immune response to maintain the homeostasis. Changes in the skin microbiota are linked to the onset and the progression of several diseases, including tumors. We characterized the skin surface and dermal microbiota of 11 dogs affected by spontaneous mast cell tumor (MCT), using skin contralateral sites as intra-animal healthy controls. The microbial profile differed between healthy and tumor skin surfaces and dermis, demonstrating that the change in microbiota composition is related to the presence of MCT. The number of observed taxa between MCT and healthy skin surfaces was detected, showing a decrease in number and heterogeneity of taxa over the skin surface of MCT, at both inter-and intra-individual level. Preliminary data on bacterial population of MCT dermis, obtained only on three dogs, demonstrated an intra-individual reduction of taxa number when compared to the skin surface. Taxonomy reveals an increase of Firmicutes phylum and Corynebacteriaceae family in MCT skin surface when compared to the healthy contralateral. In conclusion, we demonstrate that microbial population of skin surface and dermis is related to mast cell tumor. Our study provides the basis for future investigations aiming to better define the interaction between mast cell tumors, microbiota and host immune response. The epidermis, or skin surface, provides the external layer to the three parts of the skin, the inner layer being the dermis and hypodermis. The epidermis is regarded as a microenvironment containing a rich eukaryotic and prokaryotic population, currently defined as the microbiota 1,2 , which plays a role as protective and immunological barrier 3. Culture-independent determination of the microbial profile of dog skin surface has been recently determined, showing that microbiota largely differs between body sites 4. The skin microbiota is modulated by extrinsic (e.g. diet, environment) and intrinsic (e.g. genetics) factors 5 , and is not only limited to skin surface but also extends to the dermis 6. Remarkably, bacteria detected within the human healthy dermis and subcutaneous adipose tissue showed a different microbial population profile as compared to the skin surface 7. Four major phyla-namely Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes-and four major families-namely Corynebacteriaceae, Propionibacteriaceae, Staphylococcaceae, Micrococcaceae-dominate both canine 2 and human epidermal surfaces 1. Given the limited number of studies, the definition of canine skin "healthy microbiota" is still debated. Changes in microbiota composition are associated with the development of skin disorders in both humans and dogs 8,9 , as previously reported dermatitis 10 in dogs. The defensive capability of skin is supported by healthy and balanced microbiota through the interaction with the residing immune cells in the cutis 9,11,12. Due to their localization within the skin, mast cells are in close contact with the bacterial population 13. The activities of mast cells may be amplified...