There is a growing demand for exploiting cost-effective carbon sources for mixotrophic cultivation of microalgae. Fucoidan and alginate were extracted from the brown seaweed Cystoseira trinodis and were subjected to hydrolysis using H2O, HCl, or NaOH for the mixotrophic cultivation of Dunaliella salina. The algal biomass was enhanced to 0.46 g L−1 and biomass productivity reached 41.83 mg L−1 day−1 using alkali hydrolyzed alginate, which was ∼1.6-fold higher than the values under the photoautotrophic conditions. Lipid content was increased to 21.81% w/w using alkali hydrolyzed fucoidan which was 1.78-times higher than the control. Several biodiesel quality parameters were calculated and indicated that mixotrophic cultivation enhanced the biodiesel properties. The biochemical composition showed that amino acid and insoluble and soluble protein productivities were promoted 2-3-folds in relation to the control. Similarly, glycerol and soluble carbohydrate (starch) productivities were increased ∼ 1.4-times, while insoluble carbohydrate productivity was 3.3-times higher than the control. Principal component analysis demonstrated that the starch content of D. salina was reduced in compensatory of lipid accumulation. In addition, the algal growth behavior was statistically fitted using modified logistic model which indicated that lag-phase and maximum growth rate were 0.75–3.89 day and 0.019–0.066 day−1, respectively.