IAt the age of 18, Pepe along with his friend Ezequias left Brazilian youth team Corinthians Alagoano and both signed for the B team of Portuguese Liga outfit CS Marítimo, who play on the island of Madeira. After one season in the B team, where he played 10 games, Pepe was promoted to the first team for the 2002/03 season. The Brazilian's impact was incredible and he soon nailed down a place in the starting eleven, forming a formidable partnership with Mitchell van der Gaag in Marítimo's defence.

By the end of the season, under new manager Anatoliy Byshovets, Pepe started to show his versatility and adapted well to several positions including defensive midfield, attacking midfield and even as a support striker. The move by Byshovets paid off and was rewarded when Pepe scored against Sporting Braga to give Marítimo a vital 1-0 away victory.

During pre-season of the 2003/04 season Marítimo gave permission for the player to train with Sporting Club de Portugal for two weeks, after which a deal could be negotiated for Pepe's transfer. However neither club could agree on terms and the move broke down, with Pepe returning to the Madeira club shortly after.

Pepe's success continued at Marítimo and after another season he signed for FC Porto during the summer of 2004 for €1 million plus three players, Tonel, Evaldo and Antonielton Ferreira. A clause in the agreement also stated that Marítimo would received 20% of any future transfer fee.