The Pepper wreck was found on the Tagus River mouth, Lisbon, Portugal, in 1993, during an archaeological survey promoted by the Museu Nacional de Arqueologia, directed by Francisco Alves.
From 1996 to 1998 it was excavated by the Instituto Português de Arqueologia / Centro Nacional de Arqueologia Náutica e Subaquática as part of the program of the Portuguese pavilion at the 1998 world exhibition EXPO'98.
In 1999 and 2000 the remains of its hull were excavated by the Centro Nacional de Arqueologia Náutica e Subaquática, with the support of the Institute of Nautical Archaeology / Texas A&M University.
Its excavation yielded a large collection of artifacts dated from the late 16th and early 17th centuries, and lead to the tentative identification of this shipwreck as the nau Nossa Senhora dos Mártires, wrecked on September 15 1606 on its way back from Cochin, in India.
The study of its hull remains - which include a portion of the keel, eleven frames, and some of the planking - yielded interesting results and a first glance at these largely unknown ships: the Portuguese naus da India.