In this study, the performance, emission and combustion characteristics of two different biodiesel blends produced from Mahua and pongamia methyl esters were compared with conventional diesel fuel. Methyl esters for experiment were produced by using a catalytic transesterification process and, compared the properties with ASTM standard values of biodiesel fuel and diesel fuel. The experiments were performed in a four stroke, single cylinder, common rail direct injection (CRDI) system assisted diesel engine at a constant speed of 1500rpm with varying injection pressure. During the tests, the specific fuel consumption, brake thermal efficiency, combustion and exhaust emissions of the CRDI diesel engine were measured. From the results it is clear that the HC, CO and smoke levels are drastically reduced when using the methyl ester blends. Especially in the case of MME20, NOx emissions was minimum when compared with other blends and it also found less amount of other harmful emissions like HC, CO and smoke.