Ecosystem service assessment maps are an important form of data, showing the flow and characteristics of ecosystem services. However, there has been a lack of research on the spatial boundaries of synergetic and trade-off relationships among different types of ecosystem services based on the microscopic characteristics of ecosystem maps. Therefore, the boundaries of ecosystems were identified in this study using factor analysis of indicators in ecosystem service maps. Ecosystems were mapped for each indicator in each cell, and then factor analysis was used to combine all indicators into one map. Analysis of Seocheon in central South Korea shows the boundaries of two ecosystem types: a mountainous region with abundant underground water and carbon stocks that lack rice paddies, and flatlands with high crop production and a lack of scenic views. The spatial types of ecosystems in which synergy and trade-offs occur were identified by indicator, and these can be used as evidentiary material for spatial planning in order to maximize the function of each ecosystem service.