In recent years, the association between mitochondrial DNA (mtDNA) changes and tumorigenesis has been discussed. In contrast to human medicine, there are still few studies on the molecular basis of canine tumors. One of the most commonly diagnosed, solid mammary carcinoma, is characterized by its aggressiveness, difficult treatment, and generally poor prognosis. The aim of the study was to reveal mutations and polymorphisms in mtDNA in dogs with solid mammary carcinoma and to determine the relationship of these changes with the process of neoplastic transformation. Blood, healthy tissue, and neoplastic tissue samples were collected from two crossbreed dogs diagnosed with G3 and G2 solid mammary carcinoma. Subsequently, for the first time, Next Generation Sequencing (NGS) was used to analyze the whole genome mtDNA of dogs with solid mammary carcinoma. Thus, bioinformatic analyses included all 37 mitochondrial genes. As a result, 10 polymorphisms and 20 mutations were identified. Most polymorphisms/mutations were found in the dog with the more advanced stage of the disease (G3). Twelve of the thirty changes identified have not been described in the literature so far. These include eleven mutations in COX2 (m.7308A>G), ATP6 (m.8536C>T), ND4L (ins.9913_9914AG, ins.9913_9914TG, m.10165C>T), ND4 (m.10204C>T), CYTB (m.16248A>G, m.16268A>G), D-loop (m.16378G>A, m.16408G>A, m.16507T>A) which may be related to canine tumorigenesis.