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Phototrophic microorganisms have an important role in the survival, maintenance and restoration of natural ecosystems and environments, especially in arid and semi-arid areas. In this study, soil samples of Khabr National Park located in Kerman Province of Iran, were cultured onto Bold’s Basal Medium (BBM) and Blue-Green Medium (BG11). First, the isolated cyanobacteria and microalgae were purified. Following the morphological identification, molecular identifications were carried out. For this reason, genomic DNAs were extracted from the purified cultures and PCR amplification of 16s rRNA gene of cyanobacterial isolates and 18s rRNA gene of algal isolates were done. Phylogenetic relationships between these isolates sequences and the sequences retrieved from GenBank were analyzed. The results showed that cyanobacterial isolates belonged to five genera Trichocoleus, Leptolyngbya, Fischerella, Chroococcidiopsis and Stanieria. Furthermore, the green algae belonging to genera Chlorosarcinopsis, Myrmecia and Bracteacoccus were isolated from Khabr National Park. This study is a first report on isolating some phototrophs from a semi-arid ecosystem of Iran.