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Different kinds of multi-module DC-DC converters have been introduced to obviate demands for different level of voltage and power in input and output. The suitable control scheme for this type of converter necessitates equal voltage sharing for series connected modules and equal current sharing for the parallel connected modules for all operating conditions even with existence of dissimilarity in devices and components used in each module. Such a control scheme can be designed by means of linear controllers. But in the case of large variations in the parameters or considerable difference between modules of converter, linear scheme cannot accomplish equal sharing correctly. In this paper a MIMO controller scheme based on artificial neural network (ANN) will be developed to solve this problem in an input-series and output-parallel (ISOP) DC-DC converter. The proposed MIMO controller is trained using Particle Swarm Optimization (PSO). Using PSO to train the ANN based controller, eliminates the need for a prior knowledge of the system dynamics. The latter merit shows its significant usefulness when the under study system is a large multi-module system and consequently the derivation if its dynamic equations is a tedious and time consuming work. To implement the proposed controller for the ISOP converter MATLAB software will be used in this paper.