Abstract: Molecular biomarkers play a significant role in the early diagnosis of, the provision of precision therapy for, and the prognosis of hepatobiliary carcinoma. The popularity of sequencing, targeted therapy and immunotherapy for hepatobiliary carcinoma has also increased. To standardize and guide the application of molecular biomarkers in clinical practice, multiple hepatobiliary expert groups have published a consensus on the clinical application of molecular diagnosis of hepatobiliary carcinoma based on in-depth discussions, according to the current situation in China. This article will interpret the core recommendations from the consensus for hepatobiliary carcinoma diagnosis, treatment, and related quality control. We will also provide an update on progression and clarify some of the controversies surrounding molecular biomarkers based on the latest clinical guidance and research, with the aim of offering scientific references and guidance for personalized treatment decisions as well as maximizing the benefits to patients.