http://www.civil-liberties.com/pages/did_lincoln.htm

As the Civil War started, in the very beginning of Lincoln's presidential term, a group of "Peace Democrats" proposed a peaceful resolution to the developing Civil War by offering a truce with the South, and forming a constitutional convention to amend the U.S. Constitution to protect States' rights. The proposal was ignored by the Unionists of the North and not taken seriously by the South. However, the Peace Democrats, also called copperheads by their enemies, publicly criticized Lincoln's belief that violating the U.S. Constitution was required to save it as a whole. With Congress not in session until July, Lincoln assumed all powers not delegated in the Constitution, including the power to suspend habeas corpus. In 1861, Lincoln had already suspended civil law in territories where resistance to the North's military power would be dangerous. In 1862, when copperhead democrats began criticizing Lincoln's violation of the Constitution, Lincoln suspended habeas corpus throughout the nation and had many copperhead democrats arrested under military authority because he felt that the State Courts in the north west would not convict war protesters such as the copperheads. He proclaimed that all persons who discouraged enlistments or engaged in disloyal practices would come under Martial Law.

Among the 13,000 people arrested under martial law was a Maryland Secessionist, John Merryman. Immediately, Hon. Roger B. Taney, Chief Justice of the Supreme Court of the United States issued a writ of habeas corpus commanding the military to bring Merryman before him. The military refused to follow the writ. Justice Taney, in Ex parte MERRYMAN, then ruled the suspension of habeas corpus unconstitutional because the writ could not be suspended without an Act of Congress. President Lincoln and the military ignored Justice Taney's ruling.

Finally, in 1866, after the war, the Supreme Court officially restored habeas corpus in Ex-parte Milligan, ruling that military trials in areas where the civil courts were capable of functioning were illegal.