 He married in 1526 Dona Leonor Fernández de Córdoba, daughter of the 3rd Count of Cabra, who also died in 1575.They were the parents of the 3rd Marquess of Los Vélez, 2nd Marquess of Molina, etc., and Conquistador Don Luis Fajardo de Córdoba.He was the ancestor of the 1st Baron of Castellvell de Rosanés and 1st Marquess of Martorell in 1627 Don Luis Francisco Fajardo de Zúñiga, Requeséns y Girón, ?th Lord of the Majorat of Martorell in Catalonia, son of the 5th Marquesses of los Vélez.