Microalgae-derived biodiesel is commonly studied and recently gained attention as a possible substitute feedstock for production of biodiesel. In this study, the potential of marine diatoms, Cylindrotheca sp. (FPU 0031) and T. chinensis (FPU 0030), for production of biodiesel was evaluated by investigating the effect of nutrient limitation (100, 75, 50, and 25 % Roschin medium) on growth behavior response, lipid productivity, and FAME profiles of the diatom strains. The total lipid yield increased under nutrient-limited culture condition. When the concentration of the nutrient was restricted to 50 %, the average lipid yield of Cylindrotheca sp. and T. chinensis were 19.32 and 21.72 % with lipid productivity of 73.46 and 68.19 mg L−1 day−1, respectively. Nutrient limitation resulted in a decrease in biomass yield and an increase in the lipid yield of the diatom strains. The properties of biodiesel generated by the two diatoms were assessed based on FAME profiles using empirical equations. Results showed that Cylindrotheca sp. and T. chinensis conforms to the biodiesel standards specifications set by EN 14214 and ASTM D6751. The predicted properties of biodiesel observed for Cylindrotheca sp. and T. chinensis were both ideal, e.g. good cold filter plugging points (−6.94 °C and − 2.16 °C), cetane numbers (65.57 and 75.29), cloud points (1.81 °C and 7.75 °C), pour points (1.60 °C and − 4.86 °C), and low kinematic viscosities (2.89 and 2.16 mm2 s−1), respectively. Thus, suggesting the potential use of these diatoms as feedstock for producing biodiesel with high-grade fuel characteristics.