The antiviral activity in the roots of Rubia cordifolia was examined, and three naphthohydroquinones, furomollugin (1), mollugin (2), and rubilactone (3), were isolated from it. Compounds 1 and 2 strongly suppressed the secretion of hepatitis B surface antigen (HBsAg), both with IC50 = 2.0 micrograms/mL, in human hepatoma Hep3B cells while having little effect on the viability of the cells. Evaluation of structurally related derivatives of 1 and 2 revealed that a 6-hydroxy group and a pyran or furan ring contribute to this suppressive effect.