Abstract: Dunaliella is a unique group of halophilic, unicellular, eukaryotic microalgae, which is widely used in industrial field because of its rich bioactive substances such as oil, β-carotene, and polysaccharides. Dunaliella resources are diverse in the world. The morphological difference of Dunaliella species is small. Therefore, their taxonomy and identification need to be improved. Dunaliella is broad-spectrum salt tolerant, but physiological and biochemical responses of different species under salt stress are different. It is necessary to excavate the unique Dunaliella strains. We collected 20 strains of Dunaliella from home and abroad. Gene sequences of internal transcribed spacer (ITS) and cytochrome C oxidase (cox2-3) were amplified by PCR. The phylogenetic trees of Dunaliella based on the two genes were constructed by bioinformatics analysis. We used morphological methods to identify their microscopic and submicroscopic structures. Four representative indexes (max photosynthetic efficiency, neutral lipid content, β-carotene content and glycerol 3-phosphate phosphatase activity) of Dunaliella under salt stress were measured via physiological and biochemical analysis. The results showed that all algae strains belonged to Dunaliella. phylogenetic analysis of Dunaliella results based on ITS and cox2-3 given similar results. The genetic relationships of 20 Dunaliella strains were relatively close. D13 cells were the largest, and D14 cells were the smallest with a long neck. The color of Dunaliella cells was mainly green or yellow-green. The numbers of Flagella and eye-spot of them were different. D6 and D10 had the shortest growth period. The most salt tolerant strain was D18. D7 had the highest max photosynthetic efficiency. D6 and D18 had the highest dry weights of neutral lipid. D11 had the highest β-carotene content, and D7 had the strongest glycerol 3-phosphate phosphatase activity. Our research lays the foundation for the taxonomy, identification, protection, development and utilization of Dunaliella resources in the world.