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This is a pioneering GPR study to map submerged archaeological sites in the Amazon region. The GPR preliminary results for the Jenipapo site are presented in this resume. Jenipapo site is located on the Turiaçu River, Maranhão State, NE of Brazil. The region is known as Maranhense wetland where evidences of Amazonian indigenous villages from the pre-colonial period were found. The villages were lakeside dwellings supported by wooden pillars, corresponding to prehistoric stilt houses (Estearias). The objectives of this research are to refine the Estearias location and guide the search for archaeological artifacts. The results of the GPR profiles using 270 MHz showed the river bottom reflection and several diffraction hyperbolas suspended over the river bottom that are probably related to the top of the wooden pillars that supported the pre-colonial indigenous villages. This preliminary result is promising and can help to find archaeological materials.