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Single and co-culture systems of Microcystis aeruginosa and Scenedesmus obliquus were prepared with different initial algal densities and treated with different concentrations of aqueous extracts from the rhizome of Pontederia cordata to study its inhibitory effect on algal growth and the competitive relationship between these two algal species. The results showed that aqueous extracts could inhibit the growth of M. aeruginosa and S. obliquus, and the inhibition rate of aqueous extracts on the growth of M. aeruginosa was always higher than that of S. obliquus. A Lotka–Volterra competition model revealed that these two algal species can co-exist without the addition of aqueous extracts, and S. obliquus exhibited a stronger ability to compete than that of M. aeruginosa. Meanwhile, the dominant algal species changed with the addition of aqueous extracts regardless of the initial ratios of the two algae. The species ratio of mixed cultures had a strong effect on the interspecific interaction between the two algae. The higher proportion of S. obliquus in the initial proportion of two algae, the stronger competitive ability of S. obliquus when compared with that of M. aeruginosa.