To assess the toxic effects of herbicide paraquat (1,1′-dimethyl-4,4′-bipyridinium dichlorine) on the algal ecosystem, the growths of four cyanobacterial strains (Microcystis aeruginosa XW01, M. aeruginosa PCC7806, Merismopedia sp., and Synechocystis PCC6803) and two green alga strains (Chlorella pyrenoidosa, Chlorococcum sp.472) were measured with different concentrations of paraquat. The Median Effect Concentration (EC50), Lowest Observable Effective Concentration (LOEC), No Observable Effective Concentration (NOEC) and Chronic Value (ChV) of paraquat to the six strains were calculated. The experimental results showed that cyanobacteria were more sensitive than green algae to paraquat, and 96 h-EC50 value of C. pyrenoidosa was 7.4 times higher than the value of M. aeruginosa XW01. Longer exposure time displayed higher toxicity.