;Bishops of Guayaquil • Francisco Xavier de Garaycoa (1838 – 5 Sep 1851), appointed Archbishop of Quito • Tomás Aguirre (22 Jul 1861 – 14 May 1868) • José María Lizarzabaru y Borja,
SJ (22 Nov 1869 – 17 Oct 1877) • Roberto Maria Pozo y Martin,
SJ (13 Nov 1884 – 1909) • Juan María Riera,
OP (19 Jan 1912 – 20 Nov 1915) • Andrés Machado,
SJ (26 Apr 1916 – 22 Jan 1926) • Carlos María Javier de la Torre (20 Dec 1926 – 8 Sep 1933), appointed Archbishop of Quito (Cardinal in 1953) • Giuseppe Felix Heredia Zurita,
SJ (16 Dec 1937 – 2 Aug 1954) • Cesar Antonio Mosquera Corral* (11 Oct 1954 – 11 Mar 1969) • Became archbishop on 22 Jan 1956 ;Archbishops of Guayaquil •
Bernardino Echeverría Ruiz,
OFM (10 Apr 1969 – 7 Dec 1989); elevated to Cardinal in 1994 •
Juan Ignacio Larrea Holguín (7 Dec 1989 – 7 May 2003) •
Antonio Arregui Yarza (7 May 2003 – 24 Sep 2015) •
Luis Cabrera Herrera,
OFM (24 Sep 2015 – present) ;Coadjutor archbishop •
Juan Ignacio Larrea Holguín (1988-1989) ;Auxiliary bishops •
Luis Tola y Avilés (1863-1871), appointed Bishop of Portoviejo (Porto Vecchio) •
Silvio Luis Haro Alvear (1950-1955), appointed Bishop of Ibarra •
José Gabriel Diaz Cueva (1964-1967), appointed Auxiliary Bishop of Cuenca •
Vicente Rodrigo Cisneros Durán (1967-1969), appointed Bishop of Ambato •
Ernesto Alvarez Alvarez,
SDB (1967-1970 and, as Archbishop (personal title), 1980-1984), appointed Coadjutor Archbishop of Cuenca in 1970 •
Raúl Eduardo Vela Chiriboga (1972-1975), appointed Bishop of Azogues; future Cardinal •
Hugolino Felix Cerasuolo Stacey, OFM (1975-1985), appointed Bishop of Loja •
Luis Enrique Orellana Ricaurte, SJ (1978-1986), appointed Auxiliary Bishop of Quito •
Olindo Natale Spagnolo Martellozzo,
MCCJ (1990-2001) •
Victor Manuel Maldonado Barreno, OFM (1990-2003) •
Aníbal Nieto Guerra,
OCD (2006-2009), appointed Bishop of San Jacinto de Yaguachi •
Marcos Aurelio Pérez Caicedo (2006-2012), appointed Bishop of Babahoyo •
Valter Dario Maggi (2008-2011), appointed Bishop of Ibarra •
Guido Iván Minda Chalá (2009-2022) •
Giovanni Battista Piccioli (2013-2022) •
Bertram Víctor Wick Enzler (2013-2015), appointed Bishop of Santo Domingo and Ecuador •
Antonio Crameri,
SSC (2019-2021) •
Gerardo Miguel Nieves Loja (since 2021) •
Gustavo Adolfo Rosales Escobar (2022–2025) ;Another priest of this diocese who became bishop •
Eduardo José Castillo Pino, appointed Auxiliary Bishop of Portoviejo in 2012 ==Suffragan dioceses==