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The marine diesel engine is a complex system, which has the important function to guarantee the marine security. There is strong coupling relationship among the mapping process of fault diagnosis. An approach of intelligent fault diagnosis based on fuzzy neural network optimized and trained by the genetic algorithm (GA) was proposed in this paper for this system. The structure and the parameters of intelligent fault diagnosis system made up of fuzzy neural network were introduced. Through applying the genetic optimization algorithm to its weight and the threshold value that carried by the optimization training, this method may effectively show quick convergence performance. The precision of fault diagnosis also can be improved effectively. Finally this fuzzy neural network system optimized and trained by genetic algorithm was applied in the fault diagnosis of the marine diesel engine's combustion system. The simulation showed feasibility and validity of this method.