Six new prenylated flavonoids, named visconaeas A-F (1-6), and eleven known isopentenyl flavonoids (7-17) were isolated from Dodonaea viscosa (L.) Jacq. The structures of the separated compounds were determined through comprehensive spectral analysis and quantum chemical calculations. These compounds were tested for their anti-Zika virus and cytotoxicity activities. The results indicated that compound 4 showed low cytotoxicity and strong anti-Zika virus potential with EC 16.34 μM.