A simple transposition cipher was used in President Lincoln's telegram of 3 April 1865, reporting the evacuation of the last Confederate stronghold Petersburg. It is so simple that Friedman says it is "hardly worthy of a schoolboy's initial effort at preparing a secret message" (p.71) but it would indeed be a fun for schoolboys and other hobbyists in that it relies on not only letters but also pronunciation.
See another artilce for regular Federal ciphers during the Civil War.
Lincoln's cipher telegram of 3 April 1865 is as follows (Bates p.63, Plum p.35, Friedman p.71).
(Charles A. Tinker and Samuel H. Beckwith (Wikipedia) were cipher operators at the War Department and Grant's headquarters at City Point, respectively.)
Basically, this is a simple transposition cipher writing the words backwards. However, even if one reads from the back to the beginning, it does not make sense.
Actually, some words have to be transformed according to their pronunciation (or re-division of spelling).
During the last months of the Civil War, the focus of action rested on Petersburg, defended by the Confederate General Robert E. Lee. Petersburg was crucial for supply to the Confederate capital Richmond.
On 24 March, Lincoln went to Grant's headquarters at City Point responsive to Grant's invitation "for a day or two". Lincoln heard of latest development from Grant (e.g., 29 March) and relayed them to Washington (e.g., 1 April).
While Lincoln stayed longer to see the outcome of the campaign (30 March), Grant finally cut off communications of Petersburg from the outside. After the battle on 2 April, Petersburg surrendered at dawn on 3 April. The above telegram was sent at this point to inform those in Washington of the final success (Bates p.8).
Lincoln visited Grant in Petersburg on this day (The Lincoln Log). Richmond was evacuated on that evening. It was on 9 April that General Lee surrendered at Appomattox.
Cipher No. 4 was used during Lincoln's stay in City Point (Bates p.58). Then, why was this simple reversal used on this occasion instead of the regular cipher? Apparently, it was simply because Lincoln did not marked it "cipher", which can be seen in the facsimile (printed in Century Magazine, vol.74 (1907 May to October), p.295 (HathiTrust)). Bates' explanation that use of this simple mode was to avoid attracting attention of telegraph operators on the route from City Point to Washington might be understood in this light.
While Lincoln wrote most of his telegrams by himself (Bates p.123), presumably he marked "Cypher" when he thought enciphering appropriate, as seen in an image printed in Bates p.170. Probably, Beckwith, the cipher operator at Grant's headquarters thought some measures for secrecy was appropriate and used this simplest mode of scrambling. (Phonetic and irregular spelling are used even with regular ciphers (15 July 1863, Cipher No. 4; 19 June 1864, Cipher No. 2; 12 April 1865, Cipher No. 1, see another article) and cipher operators were accustomed to this.)
It is noted that this message is not marked as "Cipher" in Collected Works, while some others (8 March, 20 March, 21 March, 23 March) are. It is wondered whether other messages not marked "Cipher" were enciphered in a similar scheme.
This scheme was used on other similar occasions (Bates p.59).
A similar scheme had been used as early as November 1862 when the President considered visiting General Burnside. The message as transmitted was as follows according to Bates' recollection (Bates p.61).
Reading backwards and restoring phonetic spelling (and remembering that "flesh" is a synonym for "meat"), the following plaintext should be obtained.
This time, use of this simple scheme was resorted to because Burnside's cipher operator was temporarily absent from his post (Bates p.59).
Burnside had just taken over command of the Army of the Potomac from McClellan, whom Lincoln considered was not aggressive enough. Burnside planned to pass Robert E. Lee's Confederate army south of the Rappahannoch River and strike the Confederate capital Richmond further south. However, seeing the slow movement of the Union army, Lee concentrated his army toward Fredericksburg, a town on the Rappahannock. (Wikipedia).
The above telegram, proposing a meeting on a boat in Aquia Creek (map at Wikipedia), a tributary of the Potomac north of Fredericksburg, was sent at this timing. Lincoln did have a meeting with the general (Lincoln Log).
Whatever exchanges were made on this occasion, the Battle of Fredericksburg on 11-15 December 1862 ended in a disaster for the Union army.
Another cipher using pronunciation is described by Thicknesse, A treatise on the art of decyphering (1772), whereby a sequence of French words when pronounced by an Englishman sound like an English sentence. The scheme is used in a short story by Lilian dela Torre, "The Stolen Christmas Box."
William R. Plum, The Military Telegraph During the Civil War in the United States, vol.1 (1882) (Google)
David Homer Bates, Lincoln in the Telegraph Office: Recollections of the United States Military Telegraph Corps during the Civil War (1907) (Internet Archive) (The facsimile of Lincoln's plaintext draft is printed in Century Magazine, vol.74 (1907 May to October), p.295 (HathiTrust))
W.F. Friedman, "History of Cryptology" (pdf)
The Papers of Ulysses S. Grant, Volume 10: January 1-May 31, 1864 (PUSG) (Mississippi State University Libraries, Google)
The Collected Works of Abraham Lincoln, vol.8, the 3 April telegram
Abraham Lincoln Papers, Reply to the 3 April telegram
The Lincoln Log