Advancing or retarding pilot fuel injection timing in a diesel engine provided with either conventional mechanical fuel injection (CMFIS) or high pressure injection as in common rail fuel injection (CRDI) systems can significantly affect its performance and tail pipe emissions. Performance of diesel engine when fueled with various biofuels as well as gaseous fuels tends to vary with subsequent changes in pilot fuel injection timings. Biodiesel derived from rubber seed oil called Rubber Seed Oil Methyl Ester (RuOME) and hydrogen (H2) and hydrogen enriched compressed natural gas called (HCNG) both being renewable fuels when used in diesel engines modified to operate in dual fuel mode can provide complete replacement for fossil diesel. In the present study, effect of injection timings and venture design for gas mixing on the performance, combustion and emission characteristics of dual fuel engine fitted with both CMFIS and CRDI injection systems and operated on RuOME and HCNG/hydrogen has been investigated. Results showed that high pressure CRDI assisted injection of RuOME with optimized mixing chamber (carburetor)) for hydrogen induction in dual fuel engine performed improved compared to that with CMFIS. In addition, for the same fuel combinations, CRDI resulted in lower biodiesel consumption, lower carbon monoxide (BSCO) and hydrocarbon (BSHC) emissions and increased NOx emissions than CMFIS operation.