Acanthamoeba is a free-living amoeba and opportunistic protozoa that causes infection to humans. One of its primary infections is Acanthamoeba keratitis that occurs mostly amongst contact lens users. There are some difficulties in providing effective treatment to the patients as the cysts of Acanthamoeba spp. are very resistant towards most of the antimicrobial agents. Thus, study was conducted to determine the effectiveness of antimicrobial agents comprising 0.1% propamidine isethionate (Brolene®) and 0.3% ciprofloxacin (Ciloxan®) towards two clinical isolates of Acanthamoeba spp. (HUKM 74 and HS 72). Besides that, the minimum cysticidal concentration (MCC) of the tested antimicrobial agents were also determined. Propamidine isethionate and ciprofloxacin showed cysticidal activities at therapeutic dosage against both Acanthamoeba spp. isolates. The minimum cysticidal concentration for propamidine isethionate was between 62.5-125 µg/ml while for ciprofloxacin was 375 µg/ml. Both the clinical isolates of Acanthamoeba belonged to group II (Polyphagids).