Cancer stem cells (CSCs) are a small subpopulation of cells within tumors with capabilities of self-renewal, differentiation, and tumorigenicity when transplanted into immune-comprised mice. Accumulating evidences have shown that CSCs or tumor-initiating cells are key drivers of tumor formation and progression in both solid tumors and haematological malignancies. Identification of the CSCs or tumor-initiating cells is a fundamental and important problem in cancer research. There is still a lack of consensus regarding the existence of a "global" marker for CSCs in different human cancers, but isolated CSCs have shown both the tumor-propagating ability in immune-compromised mice and the capacity to fully recapitulate the original heterogeneity of cell types. Several cell surface markers, including CD133, CD44 and CD90, were often used to identify and enrich CSCs. Although not all types of cancer follow the CSC theory, it provides an attractive cellular mechanism to account for the therapeutic resistance and recurrence of the disease. Here we provide a brief review regarding the markers for identification of CSCs in hepatocellular cancer, allowing us to deep understand of the cellular organization of HCC and to develop therapies that target specific CSCs.