Background Dog hepatocellular carcinoma (HCC) is the most common primary liver tumor in dogs, though it remains relatively rare overall. In humans HCC is frequently resistant to chemotherapy and radiation and often shows insufficient response to immunotherapy. Its occurrence in dogs, unlike humans, is not typically associated with viral infections, cirrhosis, or alcohol consumption. These distinctions offer a unique comparative perspective on the intrinsic genetic drivers of the disease. Methods Using whole exome sequencing (WES) and single nucleus RNA sequencing (snRNA-seq) in tandem, we perform a multi-omic analysis of the dog HCC tumor. Results Mutational analysis of impactful polymorphisms revealed a conserved cross-species landscape with genes such as CTNNB1, known for highly recurrent mutations in human HCC, showing similar alterations in dogs. In dog HCC tumors, we identified the major cell types commonly observed in human HCC, including T cells, endothelial, macrophage, fibroblast, hepatocyte, and malignant characterizations. The inferred cellular communication observed across human and dog HCC cell types revealed parallels, particularly in macrophage functionality. Conclusions These findings underscore the need for expanded genetic studies of dog HCC to further elucidate cross-species commonalities, offering deeper insights into key aspects of HCC biology and identifying novel therapeutic targets.