Merkel cell tumors, a type of cutaneous round-cell tumors, are rarely observed in dogs and cats. This tumor type originates from cutaneous neuroendocrine cells. In the present study, the morphology of canine and feline Merkel cell tumors and their immunoexpression of neuron-specific enolase, cytokeratin, chromogranin A, Ki67, and metallothionein were evaluated using histopathological and immunohistochemical methods. The canine Merkel cell tumor displayed a diffuse morphological pattern, whereas the feline tumor displayed a solid morphological pattern. Both tumors were positive for neuron-specific enolase and cytokeratin, but negative for chromogranin A. The Ki67 indexes in the canine and feline tumors were 7% and 25%, respectively. The expression of metallothionein was minimal in both tumors. In conclusion, this paper describes the detailed histopathological and immunohistochemical features of uncommon canine and feline Merkel cell tumors, including metallothionein expression, which has never been studied in such tumors previously.