The endocrine-disrupting compounds, nonylphenol and bisphenol attracted much attention because of their estrogenic activity and widespread environmental distribution. The toxicity and cellular stresses of nonylphenol and bisphenol to Nannochloropsis salina were investigated. Both nonylphenol and bisphenol showed inhibited growth of N. salina, but with different degrees, in which the effective concentrations of nonylphenol 1.5 mg/l and bisphenol 10 mg/l for 5 days. Oxidative stress was induced in algal study when exposed to both endocrine-disrupting compounds as evidenced by increased malondialdehyde content than in untreated cells. Exposure also resulted in an over-expression of oxidative stress parameters was significantly affected, showing an increase in the antioxidant activities (catalase, superoxide dismutase and ascorbate peroxidase) and oxidative damage to lipids. On the other side, the profile of fatty acid methyl esters (biodiesel) has been identified as: C14:0, C16:0, C16:1, C16:2, C18:0, C18:1, C18:2, C18:3, C20:4 and C20:5. The data exhibited a clear significant effect, positively under the oxidative stress of nonylphenol and bisphenol. From the present study, we concluded that endocrine-disrupting compounds and its oxidative stress efficiently increased the individual fatty acids to meet the biodiesel standards, so the promising biodiesel feedstock from Nannochloropsis salina. Also, the oxidative stress directly affected morphological and ultrastructure of cells.