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A bibliometric analysis was applied in this work to compare SCI and EI papers on GIS. The published output analysis showed that GIS research has steadily increased in both databases of SCI and EI. The different characteristics of SCI and EI databases in journals and keywords were also discovered. It showed that we should select proper database according to the characteristics of different research purposes. This study proved that Bibliometric method can be used in the comparative studies in a specific research field.