Pollutant emissions from diesel engines have caused major impacts in disturbing the ecological system. To overcome these problems, focus is towards alternative sources. Biodiesel, derived from vegetable, non vegetables oils and algae is the future prospect. Higher viscosity is found as the major problem in use of non vegetable oil directly in engine that is removed by converting it into biodiesel by transesterification reaction. This paper discusses a detailed study on the production of Mixed Methyl Ester (MME) using a mixture consist of Schizochytrium micro algae oil and linseed oil in different volume percentage say 15:85ml through two-step trans-esterification process. An experimental test was performed to determine the efficiency and the contaminating characteristics of the diesel engine powered by blends ofMME (B10 & B20). A mixture of Schizochytrium microalgae oil and linseed oil ME (MME) is tested in a direct injection diesel engine with a single cylinder. Performance results revealed that most of the MME gave higher brake thermal efficiency and lower brake-specific fuel consumption. Emission results showed that in most cases, NOx is increased, HC and CO emissions are decreased. B10 blend of MME with diesel was found the best suitable blend for engine. Experimentally, it shows apart from its potential for implantation, that MME-powered compression ignition engine