Marques landed a penalty with the final kick of the game to earn Portugal a World Cup return for the first time since their maiden appearance in 2007, helping his side to a 16-16 draw with the United States in their final qualifier.
Appleton is expected to lead the side from centre and exciting wingers Rodrigo Marta and Raffaele Storti have also been included.
Former France international Lagisquet, who played at the 1987 and 1991 World Cups, has selected only two flyhalves in Jeronimo Portela and Joris Moura, but the versatile Marques can act as emergency cover if needed.
Hooker Mike Tadjer (34), is one of their more experienced players in the squad having spent most of his career in France’s Top14, including the last two seasons with Perpignan.
Marques had a spell with Toulouse earlier in his career and is one of three players in the squad from second-tier Beziers.
Portugal are in Pool C along with Australia, Wales, Fiji and Georgia, who they lost to in the final of the Europe Rugby Championship in March.
Their only previous appearance at the World Cup was 16 years ago when they lost all four games, conceding 209 points in the process.
Portugal Rugby World Cup squad:
Props: David Costa (GD Direito), Antonio Machada dos Santos (CF Os Belenenses), Francisco Fernandes (Beziers), Diogo Hasse Ferreira (Dax), Anthony Alves (Mont Marsan), Francisco Bruno (GD Direito)
Hookers: Duarte Diniz (GD Direito), Mike Tadjer (Perpignan), Lionel Camergue (Rugby Bassim Darcathon)
Second rows: Jose Madeira (Grenoble), Martim Belo (GDS Cascais), Steevy Cerqueira (Chambery), Duarte Torgal (GD Direito)
Back rows: Joao Granate (GD Direito), Manuel Picao (GD Direito), Rafael Simoes (CDUL), Thibault de Freitas (Floriac), David Wallis (CF Os Belenenses), Nicolas Martins (SA XV Charente Rugby)
Scrumhalves: Joao Belo (CDUP), Pedro Lucas (CF Os Belenenses), Samuel Marques (Beziers)
Flyhalves: Jeronimo Portela (GD Direito), Joris Moura (Valence Romans)
Centres: Tomas Appleton (CDUL), Pedro Battencourt (Oyonnax), Jose Lima (Narbonne)
Wings: Manuel Cardoso Pinto (Agronomia), Rodrigo Marta (Colomiers), Vincent Pinto (Colomiers), Raffaele Storti (Beziers)
Fullbacks: Nuno Sousa Guedes (CDUP), Simao Bento (Mont Marsan)
