Non-epithelial tumors only rarely affect the pancreas. In this report, we describe a malignant non-epithelial tumor with combined characteristics of malignant peripheral nerve sheath tumor (MPNST) and malignant melanoma. To more closely define the differential diagnosis of MPNST with focal pigmentation versus metastatic melanoma resembling MPNST, the tumor was investigated using histomorphology, immunohistochemistry, electron microscopy, and comparative genomic hybridization. As a result, from these analyses and from clinical findings, the diagnosis of a pancreatic MPNST with focal pigmentation was favored. However, the diagnosis of a malignant melanoma or a composite tumor could not be definitely ruled out, due to the considerable morphological and genotypical overlap between both entities, which can be explained by the close histogenetic relationship between both tumor entities.