The effects of five natural products on the growth of three harmful algae species including Chattonella marina Hara et Chihara, Alexandrium tamarense Balech and Karenia mikimotoi (Miyake & Kominami ex Oda) G. Hansen & Ø. Moestrup were observed. Four products including ε-polylysine, betaine, stachydrine and berberine exhibited selectively inhibitory effects against the three algae. However, the other product chitosan had no obvious inhibition against the above algae. Berberine and ε-polylysine exhibited relatively higher inhibitory capability against C. marina, and betaine had the highest inhibitory effect against A. tamarense. While only berberine could effectively inhibit the growth of K. mikimotoi with LC50, 120 at 3.1 mg/L. The fast inhibitory effect against K. mikimotoi and environmental safety of berberine suggested that it might be a potential algaecide against K. mikimotoi.