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The reduction of pollutant emissions of marine diesel engines can be achieved by employing multiple injection strategies, similar to the ones used in automotive engines. In the present work, the options for advanced injection strategies, in terms of pilot injections, are explored for a large two-stroke marine diesel engine operating at full load, by utilizing Computational Fluid Dynamics simulations coupled with an Evolutionary Algorithm. The goals of the present Multi-Objective constrained optimization are the minimization of nitrogen oxides (NOx) emissions and engine specific fuel consumption. The constraint, imposed by structural limitations of the engine, is the maximum cylinder pressure. The design variables include parameters controlling the pilot and main injections, and the injected total mass. The problem is handled as a Multi-Objective Optimization Problem, and the final set of elite solutions is identified based on the Pareto dominance.