Mari Luz Cortes was discovered floating in an estuary near the southern city of Huelva, 120 miles from the Algarve resort of Praia da Luz. The five-year-old vanished on January 13 when she went out to a newspaper stand.
DNA tests will be carried out on the badly decomposed remains, which were identified by her clothing.
Madeleine's parents have offered their prayers and sympathy to the girl's family. Kate and Gerry McCann, from Rothley, Leicestershire, sent Mari Luz's parents messages of support after her disappearance. The couple had also planned to include her in their poster campaign in Spain.