Histopathological diagnosis of mesenchymal tumors of the skin is based on a combination of conventional histological and immunohistochemical staining techniques with reliable cytogenetic and molecular genetic methods. Many sarcomas carry translocation-induced gene signatures (fusion genes) or characteristic gene amplifications and deletions which can be detected in formalin-fixed paraffin-embedded routine material. Fluorescence-in-situ hybridization (FISH), reverse transcriptase polymerase chain reaction (RT-PCR), and DNA sequencing (Sanger sequencing) are the preferred cytogenetic and molecular genetic techniques in a diagnostic routine setting and are widely used in conjunction with immunohistochemical phenotyping of tumor tissue. The combined immunohistochemical and molecular genetic algorithm of sarcoma diagnosis is shown in the context of dermatofibrosarcoma protuberans, malignant vascular tumors, epithelioid sarcoma, and clear cell sarcoma.