The analysis of community structures is one major research field in the science of networks. This exercise is often biased by strong hierarchical configurations as it is the case in container shipping. After reviewing the multiple definitions of port systems, this paper applies a topological decomposition method to worldwide inter-port maritime links. Isolating ports of comparable size reveals hidden substructures with the help of graph visualization. While geographic proximity is one main explanatory factor in the emergence of port systems, other logics also appear, such as specialized and long-distance trading links. This research provides interesting evidence about the role of geography, technology, and trade in the architecture of maritime networks.