Amoeba treatment of patients suffering from pri-mary amoebic meningoencephalitis caused by Naegleria fowleri has not been successful. Dam-aged morphology and effect on genes of N. fowleri as the result of its initial interaction with drug may provide clue to the success of treatment. In this study, we investigated the activity of chlorpromazine compared with amphotericin B and voriconazole against N.fowleri Khon Kaen strain using cell based assay and molecular techniques. Scanning electron and light micro-graph showed the drug interaction of treated amoebae with 0.098 ug/ml chlorpromazine was faster than 0.002 ug/ml amphotericin B and 12.5 ug/ml of voriconazole. The morphological cha-racteristics of treated amoebae with Gomori’s trichrome stain correlated to the scanning elec-tron microscope study. The effect of drugs to nfa1 and Mp2CL5 genes of treated amoebae found that at 120 min post exposure, chlorpromazine, voriconazole inhibited both genes except amphotericin B. Most of drug inhibited nfa1 except fluconazole. The results evaluated that chlorpromazine was higher potency and rapidly activity than amphotericin B and voriconazole against N. fowleri trophozoites