Perez infamously dismissed Claude Makelele's talents after allowing him to join Chelsea in 2003, while Eto'o made just three appearances before joining Mallorca and subsequently achieving superstardom at Barcelona.
Marquez, who currently counts Iker Casillas among his clients, has now revealed that he fell out with Perez over his treatment of the pair.
"It was over Makelele, for a lack of respect," he told AS when asked why their relationship ended.
"Florentino doesn’t like black players; he’s not a racist but he doesn’t like them.
"I also fought with him over Eto’o. Samuel was just as much a Galactico as Figo. He left for the colour of his skin."
Marquez also alleged that Perez affords his favourite players preferential treatment and puts pressure on his coaches to continually select the likes of Gareth Bale and Karim Benzema.
"The squad knows who [Perez's favourites] are and so does the coach," the agent added.
"The only clash he had with [former Madrid coach] Ancelotti was over Bale. He thinks that Bale is the best in the world.
"He doesn’t know how to take care of the Ballon d’Or winner [Cristiano Ronaldo] he already has in the squad. Bale is going to play wherever he likes.
"Another is Karim Benzema. He got rid of [Gonzalo] Higuain, [Angel] Di Maria, [Vicente] Del Bosque... none of whom were that bad.
"Del Bosque has won everything there is to win but what happened to him is what happened to me – he’s a not exactly a looker.
"So Florentino brought in a handsome bloke [Carlos Queiroz] who almost ruined the team."