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Civil War, Church, and State

Current day spats over church-state relations pale in comparison to the powerful legal interventions by the United States government in the southern churches during and immediately following the American Civil War, and the reactions these interventions inspired. Take the case of a Union general and a southern Episcopal bishop who squared off in Alabama in 1865.

Several denominations in the antebellum period split over the political and moral issue of slavery. Southern Methodists separated from their northern brethren, as did Baptists. Presbyterians and Lutherans suffered similar divisions. The Episcopal Diocese of Alabama declared its own constitution null and void at the diocesan convention of May 1861, and later that year joined the other Episcopal dioceses in the South to form the Protestant Episcopal Church of the Confederate States. Following the formation of a new nation, a new ecclesial structure and constitution were likewise required.

As northern troops advanced into the South, particularly in northern Alabama, the leaders of the Federal army understood the territories — including churches and their properties — as regained for northern institutional purposes. Of particular interest to military officials were the Methodist Episcopal Church, South, and the Protestant Episcopal Church which they blamed for the war. The military believed that churches and their ministers should set an example by fostering loyal sentiments to the government. Seeing few “loyal” southern ministers and certainly no “loyal” bishops, the Secretary of War in Washington, D.C., issued an order on Nov. 30, 1863, awarding all Methodist churches in the South to a Bishop Ames of the northern Methodist denomination. In another War Department order of Jan. 14, 1864, the military was directed to turn over all churches belonging to the southern Baptists to the American (northern) Baptist Home Mission Society, which the government believed to have a loyal membership. A similar order followed for the Presbyterians.

With military control of churches came attempts to control worship and prayers. The military made it illegal for churches to pray for any government official other than the President of the United States and other federal officials. Criminality was thus assigned to those who prayed for former Confederate government officials.

The first Episcopal Bishop of Alabama, Nicholas H. Cobb (1844-61), opposed secession outspokenly. But Cobb died in 1861, reportedly one hour before secession was announced. The diocese elected Virginian Richard Hooker Wilmer, a Confederate sympathizer, to succeed Cobb in the only election of a bishop held within the Protestant Episcopal Church of the Confederate States. Wilmer received his episcopal orders on March 6, 1862, at Richmond’s Monumental Church through the laying on of hands by the Bishop of Virginia, William Meade (1841-62), his assistant bishop John Johns, and Stephen Elliott, Bishop of Georgia (1841-66). Both Meade and Elliott served as presiding bishop of the short-lived Episcopal Church of the Confederate States, each dying while serving in the capacity. Bishop Meade’s death occurred eight days after Wilmer’s consecration. Wilmer’s church-state test would come at war’s end.

Once the Confederate government collapsed, Wilmer directed his clergy in a pastoral letter (or circular) to omit the “Prayer for all those in Civil Authority” from the liturgy. Wilmer later wrote in a book for his grandchildren: “I looked around and found no vestige of any such authority.” And the key term in his circular was precisely “civil authority,” incorporating several legal or canonical matters, in Wilmer’s judgment. When he was consecrated a bishop Wilmer had not declared allegiance to or conformity with the constitution and canons of the “northern” Episcopal Church because he considered only civil government (and not military occupation) lawful. The constitution and canons of both the southern and northern Episcopal churches were organized and ratified within the sphere of civil and not military governments.

The State of Alabama (known as the Department of Alabama) fell under the jurisdiction of General George H. Thomas, commander of the Military Division of Tennessee. Wilmer’s circular to his clergy went unnoticed by military officials for several months but was eventually brought to the attention of Thomas who, due to antipathies toward Wilmer, ordered a subordinate general in Mobile to investigate the matter of the directive inside Wilmer’s pastoral letter. Wilmer, for his part, viewed Thomas, a Virginian, as a traitor to their native state. When asked by a military officer when he would release his clergy to pray for the President, Wilmer countered that he would not rescind his pastoral directive at the instruction of military authority. An exchange of communication between Bishop Wilmer and military authorities ensued, the content of which seems strange if not comical when judged by the secular mindset of 21st-century America.

In perhaps the first church-state confrontation following the Civil War, Major General Charles R. Woods of Mobile issued General Order No. 381 on Sept. 20, 1865, which recited the history and details of Wilmer’s pastoral letter and the reasons for omitting the prayer for the President. Woods quoted Wilmer’s contention that prayer for the President “is altogether inappropriate and inapplicable to the present condition of things, when no civil authority exists in the exercise of its functions. Hence, as I remarked in the circular, we may yield a true allegiance to, and sincerely pray for grace, wisdom, and understanding in behalf of a government founded on force, while at the same time we could not in good conscience ask for its continuance, prosperity, etc.” But the general observed that Wilmer’s circular, issued on June 20, 1865, not only forbade prayer for the continuance of military rule but also declined to pray for anyone in authority at all. Yet the United States had a Cabinet, Supreme Court, and many other civil officials when Wilmer issued his letter, Woods noted, and Alabama subsequently acquired a civil governor.

General Thomas, through General Woods, accordingly suspended Bishop Wilmer and his clergy from their ecclesiastical functions and they were forbidden to preach or hold services. And all of the Episcopal churches in Alabama were shut down and secured. Once Wilmer and his clergy expressed proper allegiance (with evidence) to the government of the United States and took an amnesty oath they could resume their normal functions.

Wilmer, however, maintained that neither civil nor military leaders had any right or authority to interfere in church matters. Prayer was religious, not political. As he later wrote regarding the ruckus around the “Prayer for all those in Civil Authority”: “Some of the generals of the Federal army were kind enough to step forward, and attempt to solve all my doubts upon the question; but they did not succeed in settling my difficulty. … The fact that they had abrogated all the sanctions of our former legislative, judicial, and executive government only increased the necessity for more earnest prayers unto God that He would give grace to these soldiers who held us under the bayonet to ‘execute justice, and maintain truth.’”

President Andrew Johnson reluctantly advised Gen. Thomas to revoke the suspension imposed on Episcopal clergy in Alabama. Thomas did so, while offering a colorful chastisement of Wilmer, his fellow Virginian — “an individual,” wrote Thomas, who,

styling himself Bishop of Alabama, forgetting his mission to preach peace on earth and good will toward men, and being animated with the same spirit which through temptation beguiled the mother of men to the commission of the first sin — thereby entailing eternal toil and trouble on earth — issued, from behind the shield of his office, his manifesto of the 20th of June last to the clergy of the Episcopal Church of Alabama. … This man in his position of a teacher of religion, charity, and good fellowship with his brothers, whose paramount duty as such should have been characterized by frankness and freedom from cunning, thus took advantage of the sanctity of his position.

Three days later Bishop Wilmer directed his clergy to use the prayer.

As post-war readjustments continued, the General Council of the Confederate Church determined in November 1865 that each southern diocese should decide whether to rejoin the northern church. On Jan. 31, 1866, Bishop Richard Hooker Wilmer made his declaration of conformity and the Diocese of Alabama became the last to reunite with the Protestant Episcopal Church of the United States.


Fleming, Walter L. Civil War and Reconstruction in Alabama. New York: McMillan, 1905.

Perry, William Stevens. The History of the American Episcopal Church 1587-1883. Boston: James R. Osgood and Company, 1885.

Whitaker, Walter Claiborne. History of the Protestant Episcopal Church in Alabama, 1763-1891. Birmingham: Roberts & Son, 1898.

Wilmer, Richard Hooker. The Recent Past from a Southern Viewpoint: Reminiscences of a Grandfather. New York: Thomas Whittaker, 1887.

Civil War, Church, and State


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