This paper proposes a matching algorithm to find corresponding polygon feature sets between heterogeneous digital maps. The algorithm finds corresponding sets in terms of optimizing their shape similarities based on the assumption that the feature sets describing the same entities in the real world are represented in similar shapes. Then, by using a binary code, it is represented that a polygon feature is chosen for constituting a corresponding set or not. These codes are combined into a binary string as a candidate solution of the matching problem. Starting from initial candidate solutions, a genetic algorithm iteratively optimizes the candidate solutions until it meets a termination condition. Finally, it presents the solution with the highest similarity. The proposed method is applied for the topographical and cadastral maps of an urban region in Suwon, Korea to find corresponding polygon feature sets for block areas, and the results show its feasibility. The results were assessed with manual detection results, and showed overall accuracy of 0.946.