Progeny studies of Jatropha curcas and Pongamia pinnata were carried with respect to bioproductivity,pod and seed characters which is one of the selection methods in tree improvement programmes. Variations in bioproductivity and biodiesel parameters of both the plants were compared every 6 months for 4 years of investigation and analyzed by analysis of variance and correlation coefficient by Pearson’s method using software Graphpad instat 3.06(for Windows and Mac). P. pinnata has better germination rate(71.4 %), 100 pod weight(PW)(311.59 g) and 100 seed weight(SW)(173.46 g) as compared to J. curcas for germination rate(43.2 %), 100 PW(111.29 g) and 100 SW(67.46 g). P. pinnata has strong correlation for plant height to canopy growth(CG)(0.948), collar diameter(CD)(0.994), number of branches per plant(NBP)(0.995) and to number of leaves per branch(NLB)(0.862) as compared to J.curcas which showed good correlation among plant height to CG(0.976), CD(0.970), NBP(0.988), NLB(0.920) and to number of pods per branch(0.657). However, J. curcas depicted negative correlation for pod breadth to seed length(SL)(-0.447), seed breadth(-0.248) and to seed thickness(ST)(-0.364) and among the 100 PW to SL(-0.199), ST(-0.220) and to 100 SW(-0.704). About 4 kg of P. pinnata seeds were required for each liter of crude oil which yields896 ml of biodiesel on transesterification as compared to5.66 kg of J. curcas seeds for a liter of crude oil, producing about 663 ml of biodiesel. The quality of biodiesel meets the major specification of American Society for Testing and Materials(ASTM) standards for biodiesel. The crude glycerin and seed cake obtained as byproduct during biodiesel production were also measured which can be purified and used in composting, animal feeds, pharmaceuticals and cosmetic industries. Progeny studies of Jatropha curcas and Pongamia pinnata were carried with respect to bioproductivity, pod and seed characters which is one of the selection methods in tree improvement programs. Variations in bioproductivity and biodiesel parameters of both the plants were compared every 6 months for 4 years of investigation and analyzed by analysis of variance and correlation coefficient by Pearson’s method using software Graphpad instat 3.06 (for Windows and Mac). P. pinnata has better germination rate (71.4%), 100 pod weight (PW) (311.59 g) and 100 seed P. pinnata has strong correlation for plant height to canopy growth (CG The number of branches per plant (NBP) (0.995) and to number of leaves per branch (NLB) (0.862) as compared to J.curcas which showed good correlation among plant (0.948) height to CG (0.976), CD (0.970), NBP (0.988), NLB (0.920) and to nu However, J. curcas described negative correlation for pod breadth to seed length (SL) (-0.447), seed breadth (-0.248) and to seed thickness (ST) (-0.364) and The 100 PW to SL (-0.199), ST (-0.220) and to 100 SW (-0.704). About 4 kg of P. pinnata seeds were required for each liter of crude oil which yields 896 ml of biodiesel on transesterification as compared to 5 .66 kg of J. curcas seeds for a liter of crude oil, producing about 663 ml of biodiesel. The quality of biodiesel meets the major specification of American Society for Testing and Materials (ASTM) standards for biodiesel. The crude glycerin and seed cake obtained as byproduct during biodiesel production also also measured which can be purified and used in composting, animal feeds, pharmaceuticals and cosmetic industries.