We here used methylation-specific polymerase chain reaction (MSP) to study the STAP1 and AHNAK methylation level in hepatitis B patients and its correlation to the progress of HCC from BCLC stage 0 to stage C. We also explored the association of methylation level and expression level of STAP1 and AHNAK to the different stages of HCC and survival of patients using several public datasets. Here, AHNAK is linked to hepatitis B virus infection.