Amoebic keratitis is difficult to treat without total efficacy in some patients because of cysts, which are less susceptible than trophozoites to the usual treatments. The aim of this study is to evaluate the in vitro amoebicidal activity of the methanolic extracts of Satureja cuneifolia and Melissa officinalis. In the presence of methanolic extracts (ranging from 1.0 to 32.0 mg/ml), numbers of the viable Acanthamoe castellanii trophozoites and cysts were decreased during the experimental process. Both extracts showed a time- and dose-dependent amoebicidal action on the trophozoites and cysts. Among the extracts tested, S. cuneifolia showed the strongest amoebicidal effect on the trophozoites and cysts. In the presence of 32 mg/ml extract, no viable trophozoites were observed within 24 h. At the same concentration value, the extract was found effective against the cysts at a rate of 46.3% within 72 h of the experimental process. At 16 mg/ml extract concentration, no viable trophozoites were also observed in the 24th hour of the experiment. At the end of the experimental process, 34.7% of the cysts were killed by the extract. M. officinalis showed moderate amoebicidal effect. At the concentration of 32 mg/ml, 44.3% and 30.0% of the trophozoites and cysts were killed by the extract, respectively. Results obtained from these concentration values were found statistically different in terms of their actions both on trophozoites and cysts (p < 0.05).