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This article describes a design of solving ship transport optimization using tools from graph theory. The tool minimal spanning tree (denote MST) is suitable for searching ideal transport routes between the ports. The principle of the MST problem is that it describes various kinds of situations where it is necessary to use this theoretical instrument and how to use this tool for finding a solution. Graph theory knows several algorithms for searching the minimum spanning tree and this article compares two of them, in terms of their different approaches, their complementarity, and their assessment, and which of these two methods can find a feasible solution faster. To model the situation of ship transportation we use connected weighted graph where vertices represent sea ports and the edges represent the transport routes between the ports. The weight of an edge represents energy consumed to drive the boat between two ports. A theoretical discussion and a model example are carried out to compare the two methods.