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Particle Swarm and the Genetic Algorithm were coupled to optimize multiple performance metrics for the combustion of neat biodiesel in a turbocharged, four cylinder, John Deere engine operating under constant partial load. The enhanced algorithm was used with five inputs including EGR, injection pressure, and the timing/distribution of fuel between a pilot and main injection. A merit function was defined and used to minimize five output parameters including CO, NOx, PM, HC and fuel consumption simultaneously. The combination of PSO and GA yielded convergence to a Pareto regime without the need for excessive engine runs. Results along the Pareto front illustrate the tradeoff between NOx and particulate matter seen in the literature.