The vitellogenin gene expression can be altered by some estrogenic plant compounds like Genistein and β-sitosterol. Therefore, the measurement of vitellogenin gene expression can be used as an indicator to determine their effect on reproductive performance of aquatic animals. In order to evaluate the effects of genistein and β-sitosterol on the expression of vitellogenin gene in the liver and ovary of Rutilus frisii Kutum, the fish were separately exposed to 3 levels of genistein and beta-sitosterol (500, 50 and 10 ng/L). After 21 days, the RNA extracted and expression of vitellogenin gene in both the liver and ovary was investigated by Real-time PCR. The results showed the level of vitellogenin gene expression in fish exposed to genistein was higher in liver than control and β-sitosterol treatment. This difference was not observed in the ovarian tissue. Because the main site of vitellogenin synthesis expressed liver and it was controlled by endogenous estrogen (E₂), so, it seems phytoesterogenic compound such as genistein has been able to increase the relative expression of this gene in fish Exposed to 500 ng/L.