The epithelial-mesenchymal transition (EMT) has been reported to be an important program that is often activated during the process of cancer invasion and metastasis. Cancer stem cells (CSCs) that can initiate and maintain cancer are also involved in invasion and metastasis of cancer. Recently, insights into the molecular mechanisms and functional features of mesenchymal cells have been greatly colored by findings that some of them have been endowed with the self-renewal trait associated with normal tissue stem cells and CSCs. Among cancer cells experiencing EMT, only some of the most competent CSCs will succeed in planting in another organ. In this paper, we review the molecular mechanism behind the link of EMT and CSCs in cancer progression.