With Sam Sodje's loan spell over and captain Richard Naylor injured, Marques found himself as first choice central defence partnership with Patrick Kisnorbo at the start of the 2009–10 season. However, Marques lost his starting place when he suffered an Achilles injury while on international duty in September, and dropped down the pecking order when he was out injured when Leeds completed the signing of Leigh Bromby. Marques' injury kept him out for a prolonged period lasting over several matches. After featuring in some reserve matches and closed-door friendlies, Marques returned from injury and was named to the substitutes' bench against Kettering Town. After his spell out injured, he was behind Patrick Kisnorbo, Richard Naylor, Leigh Bromby and Ľubomír Michalík in the pecking order for Leeds. Marques was named on the bench against Oldham Athletic and kept his place on the bench against Huddersfield Town. When Naylor and Kisnorbo both became fit, they returned to the starting lineup, with Michalík dropping to the substitutes' bench at Marques' expense.