Tumors of mesenchymal origin, also called soft tissue tumors, include tumor from muscle, fat, fibrous tissue, vessels and nerves, which are a group of heterogeneous neoplasms, and accounts for about 1% of all malignant tumors. They are uncommon tumors in routine practice, with complex tumorigenesis. Due to the recent advance in molecular pathology, we got a major achievement in the understanding of these tumors at the gene level, which makes the diagnosis and prognosis of this type of tumor more accurate and comfortable. This chapter will cover some molecular pathology and diagnosis of soft tissue and bone tumors.