In this study, the effects of several ionic liquids and traditional organic solvents on the growth of the green microalga, Selenastrum capricornutum, were investigated. The toxicities were strongly related to the incubation time and chemical structures of the ionic liquids. The toxicities of tetrabutylphosphonium and tetrabutylammonium containing bromide anion were observed to decrease when the incubation time was raised from 48 to 96 h. Conversely, the toxicities of 1-butyl-3-methylimidazolium and 1-butyl-3-methylpyridinium containing bromide anion were found to increase with increasing incubation time. Of the ionic liquids tested, 1-butyl-1-methylpyrrolidinium bromide was found to be the least toxic, which is similar in toxicity level of dimethylformamide. In general, the toxicities of the ionic liquids were estimated to be two and four orders of magnitude greater than those of the organic solvents examined, although ionic liquids are being considered as green solvents.