An intelligent hybrid Taguchi-genetic algorithm (IHTGA) is used to optimize bearing offsets and shaft alignment in a marine vessel propulsion system. The objectives are to minimize normal shaft stress and shear force. The constraints are permissible reaction force, bearing stress, shear force, and bending moment in the shaft thrust flange under cold and hot operating conditions. Accurate alignment of the shaft for a main propulsion system is important for ensuring the safe operation of a vessel. To obtain a set of acceptable forces and stresses for the bearings and shaft under operating conditions, the optimal bearing offsets must be determined. Instead of the time-consuming classical local search methods with some trial-and-error procedures used in most shipyards to optimize bearing offsets, this paper used IHTGA. The proposed IHTGA performs Taguchi method between the crossover operation of the conventional GA. Incorporating the systematic reasoning ability of Taguchi method in the crossover operation enables intelligent selection of genes used to achieve crossover, which enhances the performance of the IHTGA in terms of robustness, statistical performance, and convergence speed. A penalty function method is performed using the fitness function as a pseudo-objective function comprising a linear combination of design objectives and constraints. A finite-element method is also used to determine the reaction forces and stresses in the bearings and to determine normal stresses, bending moments, and shear forces in the shaft. Computational experiments in a 2200 TEU container vessel show that the results obtained by the proposed IHTGA are significantly better than those obtained by the conventional local search methods with some trial-and-error procedures.INDEX TERMS Marine vessel propulsion system, bearing offsets, shaft alignment, optimal design, genetic algorithm.