Nowadays marine transportation system has been demonstrated as a dominant support for global economy and there has been so severe competition among ports and shipping industries. To take economies of scale into consideration, there has been a remarkable growth of ship sizes. The resulting massive flow has reduced unit-shipping cost. However, it has increased the cost in port as a dominant part of the total cost. Hence, discount policy in port cost is worth to note. In this paper a genetic algorithm-based analysis is conducted for marine transportation network that consider discount model for port-related charge. In this discount model, discount rate is a function of bundled flows in the interhub links, which are characterized by non-linearity and thus is hard to solve. The result shows that bundled flows tend to several big hub ports and results in reduced total cost for the entire network system.