As well as Fernandes, two others are charged with murder: LuizHenrique Ferreira Romao, known as Macarrao, and former policeman Marcos Aparecido dos Santos, known as Bola.
The warrants were issued after a 17-year-old cousin of Mr Fernandes told police that he had taken part in Ms Samudio's abduction with a friend of the footballer, LuizHenrique Ferreira Romao.