The ultrastructure of free living amoeba isolated by axenic cultivation from water sources in Egypt was studied .Naegleriatrophozoites showed endoplasmic reticulum around the nucleus similar to the non pathogenic variant Naeglerialovaniensis while Acanthamoebatrophozoites have cell coat ,spiky pseudopodia and encircling nucleus with rough and smooth endoplasmic reticulum .So it could be concluded from ultrastucture study and experimental infection , that both NaegleriaandAcanthamoebastrains isolated from different localties in Egypt are non pathogenic