Nowadays the microalga Dunaliella salina is getting increasing attention because of its beta-carotene production, its applications in food, pharmaceutical and cosmetic industries as well as genetic engineering. Therefore isolation and identification of high productive species would be very useful. The main goal of this research was to collect the local Dunaliella and to study genetic diversity within the species of Dunaliella salina based on 18S rDNA gene and AFLP marker. Sampling was performed from different areas of saline waters of Iran including Urmia, Qom, Gavkhuni and Maharlou. Polymerase Chain Reaction was performed using conserved primers of 18S rDNA gene in Dunaliella genus. In total 100 isolate were obtained. The isolates were divided in three groups based on 18S rDNA. In group 1, a fragment of 1770bp, in group 2 a fragment of 2170 bp and in group 3, a band of 2570 bp were produced as 18S rDNA.

The isolates of group 2 by 18S rDNA size of 2170 bp, were studied using AFLP marker. Based on cluster analysis and the resulted dendrogram, the isolates were located in 4 individual groups. Group A mainly involved standard strain of Dunaliella salina 19/18 together with the isolates of Maharlou, Urmia, Gavkhuni and Qom. Group B involved isolates of Sharafkhaneh region of Urmia lake. The isolate of Chichest region of Urmia lake individually placed in group C. Group D contained the isolates of Urmia, Gavkhuni and Qom.

Altogether, the isolates which were close to the standard isolate based on AFLP data, can be introduced as the species Dunaliella salina. Although, some isolates are similar to Dunaliella salina considering the size of 18S rDNA, they may not belong to this species. Therefore, sequencing of 18S rDNA and investigation of ITS region is necessary for the final precise conclusion.