Public concerns regarding the use of copperbased algaecide for controlling problematic algae may arise due to the risks it creates to non-target algae. To examine this concern, a series of comparative algal toxicity experiments were conducted to study effects of prokaryotic and eukaryotic algal cell densities on their responses to exposures of copper sulfate and copper-ethanolamine (Cu-EA). Microcystis aeruginosa and Pseudokirchneriella subcapitata were cultured separately in BG 11 medium to three initial cell densities (5 × 10 4 , 5 × 10 5 , and 5 × 10 6 cells/mL). The 96-h EC 50 values of copper sulfate for M. aeruginosa at the three cell densities were 9, 63, and 112 μg Cu/L, respectively; and were 192, 1873, and 4619 μg Cu/L for P. subcapitata. The 96-h EC 50 values of Cu-EA were 101 and 2579 μg Cu/L for M. aeruginosa and P. subcapitata at 10 6 cells/mL. The margin of safety (MOS) for P. subcapitata at 10 4 cells/mL was 1.3, 0.9, and 0.8 when M. aeruginosa cell density was 10 4 , 10 5 , and 10 6 cells/mL. This laboratory study suggests that applying copper-based algaecides to control problematic algae at a relatively low cell density would inhibit their growth with minimum impacts on non-target algae; risks to non-target algae would increase with increases of problematic algal cell density.