The efficiency of cyanobacterial strains as biodiesel feedstock varies with the dwelling habitat. Fourteen indigenous heterocystous cyanobacterial strains from rice field ecosystem were screened based on growth kinetic and fuel parameters. The highest biomass productivity was obtained in Nostoc punctiforme MBDU 621 (19.22 mg/L/day) followed by Calothrix sp. MBDU 701 (13.43 mg/L/day). While lipid productivity and lipid content was highest in Nostoc spongiaeforme MBDU 704 (4.45 mg/L/day and 22.5% dwt) followed by Calothrix sp. MBDU 701 (1.54 mg/L/day and 10.75% dwt). Among the tested strains, Nostoc spongiaeforme MBDU 704 and Nostoc punctiforme MBDU 621 were selected as promising strains for good quality biodiesel production by Preference Ranking Organization Method for Enrichment Evaluation (PROMETHEE) and Graphical Analysis for Interactive Assistance (GAIA) analysis.