The identification of blue-green algae is a paramount importance step due to their significant role in various ecosystems and potential implications for human health. Four species of blue-green algae were molecularly and morphologically identified; three species of which were identified for the first time locally in the water bodies in Basrah southern the Republic of Iraq, represented by Cyanobacterium aponinum,  Leptolyngbya halophile and Chroococcidiopsis cubana. The fourth species, Gloeocapsa calcarea, is registered for the first time in the GenBank on the NCPI website. A phylogenetic tree was designed based on the 16S rRNA gene sequences using the Neighbor-Joining method through molecular evolutionary genetics analysis Version 11. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test are displayed next to the branches. The tree showed that the strains were closely related to their respective reference strains.