Biodiesel is a renewable alternative to petro-diesel used in compression ignition (Cl) engine. Two B100 biodiesel samples were prepared by patented routes from the lipids extracted from marine microalga Chlorella variabilis (BA) cultivated in salt pans and wasteland-compatible Jatropha curcas (BJ). The fuels complied with ASTM D-6751 and European Standard EN-14214 specifications. Standard Petro-diesel served as a control. Transient performance and emission characteristics of a heavy duty diesel engine fuelled with these B100 fuels (RI and BA) were studied over European Transient Cycle. Test results showed that both B100 biodiesels outperformed petro-diesel in terms of particulate matter (PM), carbon monoxide (CO) and hydrocarbon (HC) emissions, with slight penalty on NOx emissions. Among the two biodiesels, merits of BA were established over BJ in terms of nitrogen oxides (NOx) emissions and specific fuel consumption. Mode-wise transient emission analysis revealed that NOx was highest in rural mode, CO was highest in urban and HC was highest in motorway mode for all fuels. BA may be considered as a promising alternative fuel for diesel engine which can be produced sustainably through cultivation of the marine microalga in coastal locations using seawater as culture medium, obviating thereby concerns around land use competition for food and fuel. (C) 2015 Elsevier Ltd. All rights reserved.