The microalgae, Amphora sp < /em>., are great sources of several beneficial secondary metabolites as vitamins, phenolic compounds, flavonoids and carotenoids. The present investigation aimed to introduce molecular and microscopic characterization for one Amphora isolate obtained from Moshtohor irrigated channels, Qalyubia governorate, Egypt, (30.35N 31.22E). The obtained isolate was cultured and purified using selective medium (F2 medium), also, it has been identified genetically by sequencing of 18S rRNA gene and deposited in NCBI database under the accession number (MN606209.1). Phylogenetic analysis results revealed an identify ratio (98.54%) with the nearest sequence, Amphora ovalis (KJ463437.1), deposited in NCBI Gen Bank.