Two Naegleria species were isolated and identified from various water sources in Lower and Upper Egypt. Identification was based on the morphology, nuclear division and the excystation and flagellation tests. The trophic, cystic and flagellate forms of N. gruberi are larger than those of N. fowleri and the cyst of the former species has one or more pores while that of the latter species has no pores and has an outer gelatinous layer. The size and the morphological characteristics of these two free-living amoebae from Egypt were in complete agreement with those previously described for amoebae of this same genus and species endemic to other geographical areas.