Naegleria fowleri was causative agent of primary amoebic meningoencephalitis (PAM). Accroding to the failure of treatment, several researches reported the activity of chemotherapeutic drugs against N.fowleri but we did not know the drug resistance of the amoebae. The purpose of this study was to examine the effects of drugs (amphotericin B, artesunate, azithromycin, voriconazole, chlorpromazine, fluconazole and gentamicin sulphate) on ITS and pB2.3 genes of Naegleria fowleri trophozoites. Our study demonstrated gene expression of treated N.fowleri by RT-PCR. The results reviewed that ITS gene of N. fowleri showed up regulate to amphotericin B, azithromicin and gentamicin sulphate, while pB2.3 gene showed up regulate to artesunate. These results compared with beta actin (house keeping gene) expression at time intervals 15 - 120 min. The change of gene expression of treated N.fowleri was possibly to cause of drug resistance. The mechanism of drug resistance genes ITS and pB2.3 of N.fowleri should be clarified in further study.