Berberine, as an allelochemical extracted from golden thread (Coptis chinensis), inhibits the growth of Microcystis aeruginosa significantly. To assess berberine-induced damage on the algal photosynthetic apparatus, the effects of berberine on the algal photosynthetic pigments compositions and ultrastructure were investigated. The results showed that the relative chlorophyll a content of M. aeruginosa decreased with the increasing concentrations of berberine and the prolongation of exposure time. The relative contents of phycocyanin, allophycocyanin and phycoerythrin of M. aeruginosa transitioned from a decrease to an increase in the early phase of the experiment, and then decreased sharply to the end at low concentrations. However, when berberine concentration raised to 20.0 mg·L-1, all the relative phycobilins contents of M. aeruginosa had been decreasing with the prolongation of exposure time. Of the three phycobilins of M. aeruginosa, phycocyanin was affected most severely by berberine. TEM photographs showed that the ultrastructures of the multiple-layered cell wall, cell membrane and thylakoid lamella of M. aeruginosa were destroyed severely under the stress of berberine with the occurrence of cyanophycin granules. It was concluded that decreases in the photosynthetic pigments and destruction of the algal cells ultrastructures might be involved in berberine-caused antialgal mechanism.