Freshwater Benthic algal samples were collected from seven governorates in the Nile Delta (1- El-Sharkia. 2- El-Gharbia. 3-El-Dakahlya. 4- Damietta. 5-El-Menofia. 6- El-Beheira. 7-Kafr El-Sheikh.) in addition to El-Fayum governorate during the period 2001-2004. The study was made for collecting and identifying as much as possible of the diatom species which occur in the different freshwater benthic habitats. A total of 220 taxa related to 38 genera were identified during this work, 199 taxa from the different localities in Nile Delta and 144 taxa from El-Fayum. The distribution and mean frequencies of diatoms in the sampling localities of the studied area were done. Most of species recorded in this investigation were oligohalobous cosmopolitan. This study showed also that Cyclotella meneghiniana, C. ocellata, Cocconeis placentula, Melosira granulata, Nitzschia palea, N. obtusa and N. obtusa var. scalpelliformis were the most prominent species in Nile Delta and El-Fayum. Ecological data as well as dimensions and photomicrographs of 29 taxa using LM and SEM were made.