Luis Maldonado, O.F.M. Obs. (30 Aug 1595 Appointed - 1596 Died)

​Francisco Ortega, O.S.A. † (13 Sep 1599 Appointed - 1602 Died)

Baltazar de Covarrubias y Múñoz, O.S.A. † (13 Jan 1603 Appointed - 6 Jun 1605 Appointed, Bishop of Antequera, Oaxaca)

​Pedro de Godinez, O.F.M. † (12 Dec 1605 Appointed - 1611 Died) ​

Pedro Matías, O.F.M. † (17 Sep 1612 Appointed - 1615 Died)

Diego Guevara, O.S.A. † (3 Aug 1616 Appointed - 1621 Died)

Luis de Cañizares, O.M. † (1 Jul 1624 Appointed - 19 Jun 1628 Appointed, Coadjutor Bishop of Comayagua)

Francisco de Zamudio y Avendaño, O.S.A. † (10 Jul 1628 Appointed - 27 Apr 1639 Died)

Nicolás de Zaldívar y Zapata, O.S.A. † (2 May 1644 Appointed - 1646 Died)

Antonio de San Gregorio, O.F.M. † (17 Nov 1659 Appointed - 1661 Died)

Andrés González, O.P. † (10 Sep 1685 Appointed - 14 Feb 1709 Died)

Domingo de Valencia † (10 Jan 1718 Appointed - 21 Jun 1719 Died)

Felipe Molina y Figueroa † (20 Nov 1724 Appointed - 1 May 1738 Died)

Isidro de Arevalo † (29 Aug 1740 Confirmed - 1751 Died)

Manuel de Matos, O.F.M. Disc. † (11 Feb 1754 Appointed - 24 Feb 1767 Died)

Antonio de Luna, O.F.M. Disc. † (19 Dec 1768 Appointed - 16 Apr 1773 Died)

Juan Antonio Gallego y Orbigo, O.F.M. Disc. † (14 Dec 1778 Appointed - 15 Dec 1788 Appointed, Archbishop of Manila)

Domingo Collantes, O.P. † (15 Dec 1788 Appointed - 23 Jul 1808 Died)

Bernardo García y Hernández (Fernandez Perdigon), O.F.M. Disc. † (23 Sep 1816 Appointed - 9 Oct 1829 Died)

Juan Antonio Lillo, O.F.M. Disc. † (28 Feb 1831 Confirmed - 3 Dec 1840 Died)

Vicente Barreiro y Pérez, O.E.S.A. † (19 Jan 1846 Confirmed - 14 Apr 1848 Confirmed, Bishop of Nueva Segovia)

Manuel Grijalvo y Mínguez, O.E.S.A. † (14 Apr 1848 Confirmed - 13 Nov 1861 Died)

Francisco Gainza Escobás, O.P. † (25 Sep 1862 Confirmed - 31 Jul 1879 Died)

Casimiro Herrero Pérez, O.S.A. † (1 Oct 1880 Appointed - 12 Nov 1886 Died)

Arsenio del Campo y Monasterio, O.E.S.A. † (25 Nov 1887 Appointed - 7 Apr 1903 Resigned)

Jorge Barlin y Imperial † (14 Dec 1905 Appointed - 4 Sep 1909 Died)

John Bernard MacGinley † (2 Apr 1910 Appointed - 24 Mar 1924 Appointed, Bishop of Monterey-Fresno, California)

Francisco Sales Reyes y Alicante † (20 Jun 1925 Appointed - 15 Dec 1937 Died) ​

Pedro Paulo Songco Santos † (21 May 1938 Appointed - 6 Apr 1965 Died)

Teopisto Valderrama Alberto † (6 Apr 1965 Succeeded - 20 Oct 1983 Resigned)

Leonardo Zamora Legaspi, O.P. † (20 Oct 1983 Appointed - 8 Sep 2012 Retired)

Rolando Octavus Joven Tria Tirona, O.C.D. (8 Sep 2012 Appointed -  Present)