 He made his Süper Lig debut on 11 September in a 1–1 home draw against Manisaspor, and scored his first goal late in the month in a 2–1 home loss against Galatasaray.In August 2006, after his team's relegation, Rafael Marques agreed to a contract with Manisaspor, suffering the same fate in his second season.During the 2008–09 campaign, he contributed with twelve goals as his side was crowned champions and returned to the first division at first attempt.