Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death worldwide. Patients with HCC generally present at an advanced stage resulting in death within 6-20 months. Therefore, novel treatment modalities and sensitive prognostic markers that can decrease the mortality rate of HCC are required. HCC is a complex and heterogeneous tumor with multiple genetic aberrations. It has been well described that accumulation of genetic and epigenetic changes leads to the clonal selection of cancer cells harboring aggressive tumor behavior. Aberrant expression of cancer-related genes is one of the hallmarks of cancer cells and plays a role in hepatocarcinogenesis. Epigenetic alterations, such as the alteration of DNA methylation and histone modification in cancer cells, can also induce the activation and inactivation of cancer-related genes. Studies have shed light on the link between HCC-related genes and molecules, and a better understanding of the mechanisms of HCC pathogenesis could be translated into clinical biomarker tools. Moreover, analyses of genetic and epigenetic alterations have identified potential biomarkers that might be targeted therapeutically. In this review, we update the current knowledge of biomarkers in HCC, examine recently published literature, and introduce some representative molecules in each category.