Unlike other weapon systems, a naval vessel has unique characteristics in that the vessel itself is a naval unit. In limited space, compartments with various objectives and characteristics need to be arranged, so that vessel performance is maximized. This paper studied a compartment arrangement algorithm that considers activity relationships among compartments and survivability of a vessel. Based on the study, a compartment arrangement application is developed that can generate various layout alternatives swiftly. The application developed in this study aims at automating a two dimensional compartment layout problem. A combinatorial optimization is performed with the differential evolution algorithm to achieve the optimized layout.