A total of 48 samples from two different water bodies;24 from fresh and 24 from marine waters (Alexandria) were collected, filtered, cultured on non-nutrient agar, and incubated at 37ºC for the presence of potentially pathogenic FLAs. Amoebae were isolated and identified by means of their morphological characteristics of both trophic and cyst stages. After collection for one year, it was found that freshwater samples had a higher occurrence of FLAs (83.3%) than seawater samples (37.5%).  The highest occurrence percentage of FLAs was 100% in freshwater and 83.3% in seawater samples in summer, while their lowest values reached 66.7% and 16.7% in autumn Respectively. Morphological identification of these isolated amoebae revealed the presence of FLAs belonging to 5 genera namely Acanthamoeba, Naegleria, Vahlkampfia, Vermamoeba as well as Vannella.