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The Punta del Este and Pelotas Basins are located on the southeastern margin of South America. They are bounded by important geological features and structures related to the opening of the South Atlantic Ocean during the breakup of Gondwana. Integrated geophysical data analysis, including magnetic and gravity data, has been used to subdivide the basins into four domains and identify well-defined fracture zones. The northernmost domain is characterized by the Florianópolis High and the Torres High, which have a high magnetic amplitude and a positive gravity anomaly. The Rio Grande Submarine Fan and Mostardas Low characterize the central domain. The South domain is primarily characterized by the presence of the Polonio High, exhibiting a moderate to high intensity in gravimetric values. The Punta del Este Basin exhibits a relatively uniform magnetic relief characterized by small and irregular anomalies. The integrated interpretation of geophysical data enhances our understanding of the subsurface geology. It provides valuable insights for further geological investigations and resource exploration in the Punta del Este and Pelotas sedimentary basins along the South Atlantic margin.