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The combination of cultivation and molecular methods had allowed for identification of the major haloalkaliphilic archaeal species in soda lakes of Wadi Natrun in Egypt. The archaeal diversity in the water and sediment samples of four Soda lakes of Wadi Al-Natrun was assessed by shotgun metagenomic sequencing, for DNA extracts from the environmental samples for studying community structure and functional analysis. In addition to enrichment and isolation on seven different complex and defined media.the community analysis revealed predominance of domain archaea (82%),including phylum Euryarchaeota, family halobacteriaceaeas, A wide array of Archaea, was detected, Halorubrum is the most dominant species representing 32% of Archaeal species, While Eubacteria comprised only 2% with total reads 157 of microbial community; Bacteraidetes (1.2%), Proteobacteria (0.3%), Firmicutes (0.1%), Chloroflexi (0.2%) and Actinobacteria (0.2%). And only 17% were unassigned, Metagenome sequence information is available at EBI under EBI Metagenomic database with an accession number PRJEEB18746.