The effect of phenanthrene (PHE) as a polycyclic aromatic hydrocarbon (PAH) on the green microalgae Chlorella vulgaris was studied. After exposure of the algal cells to different concentrations (2, 10, 25 and 50 ppm) of phenanthrene for 7 days, a significant increase occurred in the activity of the antioxidant enzymes including ascorbate peroxidase (APX), catalase (CAT) and superoxide dismutase (SOD). In addition, PHE treatments resulted in an increase in total phenol and flavonoid contents as non-enzymatic antioxidant compounds. Intriguingly, the cell density, dry weight and fresh weight of algae were enhanced at 2 ppm of PHE in comparison to control. However, the growth parameters as well as the photosynthetic pigments content of C. vulgaris gradually decreased with the enhancing concentration of phenanthrene. Flow cytometric analysis showed no significant reduction in the viability cell in the samples exposed to 50 ppm of PHE for 24 h, while chlorophyll fluorescence was significantly reduced. Furthermore, distorted morphological symptoms of cell structure were observed through scanning electron microscopy (SEM) analysis in a number of cells exposed to 50 ppm of PHE. These findings revealed that C. vulgaris possesses significant resistance against phenanthrene as a PAH pollutant. Mainly, the algal cells fight the toxicity by the increasing activity of antioxidant systems in order to diminish the effects of reactive oxygen species (ROS).