FFK29 is a synthetic class II HDACi (Histone deacetylase inhibitors) which have have recently emerged as novel therapeutic options for treating various protozoan and parasitic diseases. While these HDACi demonstrated a negligible effect on the viability of mature cysts, Acanthamoeba encystation was significantly inhibited by these HDACi. In conclusion, these synthetic HDACi demonstrated potent amoebicidal effects and inhibited the growth and encystation of Acanthamoeba, thus highlighting their enormous potential for further development.