Abstract. In search of an ecofriendly algaecide, aqueous extracts of two medicinal plants, Thymus satureioides Coss. and Artemisia herba alba L., were assessed for antialgal activity against Microcystis aeruginosa. An experiment was designed using five treatments (1%, 0.75%, 0.5%,0.25% and 0.1%). The growth of M. aeruginosa, morphological modifications, and photosynthetic pigments (chlorophyll a and carotenoids) on exposure to the extracts were explored. Also, phytochemical parameters in the extracts were analyzed to reveal the potential allelochemical compounds.The results showed that both T. satureioides and A. herba alba extracts inhibited the growth of M. aeruginosa in a concentration-dependent way. After 8 days of treatment, the highest inhibition rates reached were 95%, 93% and 88.58%, and for T. satureioides and A. herba alba aqueous extracts, respectively. Chlorophyll a and carotenoid concentrations in cultures decreased especially in the 1% treatment group. Several morphological changes were observed in the treatment group compared to the controls. It was concluded that M. aeruginosa growth was suppressed by the potentially allelochemical compounds and probably by other allelochemical substances in aqueous extracts. Our results illustrated that both T. satureioides and A. herba alba extracts are able to control Microcystis blooms, and these may be recommended as a remedy for contamination of water bodies by harmful blooms.