Civil War Encounters Touring the West: Part Three – Rebel Prisoners on Alcatraz Island

Part of a Series

After leaving Virginia City, Nevada, and stopping to see Lake Tahoe, my wife Brittany and I continued our road trip west to San Francisco. It may not seem apparent, but San Francisco has the richest Civil War history on the Pacific coast. One of the most visible signs of that wartime history is there for all to see in the middle of the bay, Alcatraz Island.

San Francisco boomed following the discovery of gold in 1848, so much so that it soon became “the equal of any other city,” thanks to its “large streets, magnificent buildings of brick, and many even of granite, built in the most substantial manner.”[1] In 1849, the city numbered less than 1,000 inhabitants. A year later, it was 35,000! All the mineral wealth mined in the 1850’s made the port a vital location during the Civil War. It was here that all gold and silver mined in California, Oregon, Washington, and Nevada was kept before being shipped via the Pacific Mail Steamship Company to the isthmus of Panamá. There the bullion crossed on the Panama Railroad before boarding steamers of Cornelius Vanderbilt’s Atlantic and Pacific Steamship Company for final transportation to New York City.

Panorama of San Francisco Bay showing the Golden Gate Bridge (right), San Francisco (center), and Alcatraz Island (left).

During the Civil War there were fights to control this Panamá route, with Confederate commerce raiders and privateers seeking out the steamers carrying gold. That activity resulted in some of the first prisoners kept at Fort Alcatraz, which later became the famed prison. Two groups of Confederates in particular, the leadership from the privateer Chapman and the team of Confederate sailors known as the Salvador Pirates, made Alcatraz their home before being put on trial.

The privateer Chapman was an odd one in that it was acquired and prepared for sailing from San Francisco itself. Several Confederate sympathizers organized the venture, with one leader, Asbury Harpending, even going to Richmond to receive a letter of marque. They purchased the small sailing vessel Chapman in early 1863 and quietly made plans for it to sail. Their plan was to depart San Francisco with a hold filled with uniforms and weapons, land a port in Mexico where they would process and forward their letter of marque, then sail the Panamá route until they could hopefully capture a Pacific Mail Steamship Company treasure ship. United States sailors and revenue officers, and San Francisco police and port authorities tracked their preparations and Fort Alcatraz’s commander was instructed to prepare “to receive and hold as prisoners” anyone captured on Chapman.[2] The morning of their scheduled departure from San Francisco, March 15, 1863, the ship was captured by tugs packed with local police and small boats filled with sailors from USS Cyane.

Asbury Harpending spent time at Alcatraz in 1863 for helping outfit the proposed Confederate privateer Chapman. (The Great Diamond Hoax)

In late 1864 another incident occurred when Confederate Navy Acting Master Thomas Hogg took a team of specially enlisted sailors to the Panamá isthmus. Disguised as civilian passengers, they booked passage for a trip north to California, with the goal of seizing it from within and using it to then capture other treasure ships heading south packed with bullion. U.S. intelligence networks tracked the Confederates in the Caribbean and Panamá isthmus. They diverted one ship to stall their plan. When the Confederates boarded the steamer Salvador in November 1864, sailors from USS Lancaster waited for it to enter international waters and quickly detained Hogg and six conspirators.

Alcatraz Island, taken from the shore in 1866. (Library of Congress)

Both Chapman’s crew and the Salvador Pirates were taken to Fort Alcatraz, the island fortification protecting San Francisco Bay. When asked what charges would be brought against them upon landing at Alcatraz, Chapman’s leaders were told “Why, piracy of course.”[3] They were separated, searched, and interrogated before being isolated and confined in separate “lath and plaster” rooms.[4] Chapman’s leaders were not charged with piracy, and after a short stay in Alcatraz, they were moved to the San Francisco jail. Based on President Lincoln’s Second Confiscation Act, three of the leaders instead faced civil charges of “engaging in, and giving aid and comfort to, the then existing rebellion against the government of the United States providing aid to the rebellion against the United States.”[5] The remaining crew was let free after taking an oath of allegiance.

The three were found guilty and sentenced to ten years in prison, but within a year they were all free. Being a British citizen, one was returned to England upon the demand of a member of the British Parliament. The other two sued for release after President Lincoln issued an amnesty policy in December 1863, and were free men in 1864.

Being captured near the Panamá isthmus, the Salvador Pirates were transported to San Francisco on USS Saginaw, and upon arriving were indeed “confined in military custody, subject to trial by military court-martial” at Alcatraz.[6] They were placed in a single 10 foot by 20-foot cell with a few open embrasures offering limited light and views of the harbor.[7] They received straw mattresses and rations, but could not leave their common room until the fort’s doctor urged open-air exercise to prevent sickness.

USS Saginaw (center) transported Confederate sailors from the Panama isthmus to Alcatraz. (NH 2012, Naval History and Heritage Command)

In May 1865, Major General Irvin McDowell convened a military tribunal for the Salvador pirates. Just like Chapman’s leaders, they were transferred from Alcatraz to San Francisco’s jail. In June Hogg and his six fellow Confederates were found guilty and sentenced to death by hanging. The tribunal specifically explained how they held authority to do so, affirming in their final statement that the Salvador Pirates “have not been tried by the military court as citizens of the United States violating its statute laws, but as belligerent enemies to the United States for a violation of the rules of war” by illegally boarding a ship in a foreign port intending to seize it.[8]

The reason we do not remember the Salvador Pirates alongside the Lincoln assassination conspirators and Captain Henry Wirz of Andersonville prison for being executed at the end of the war was because General McDowell commuted their sentences. Hogg instead was sentenced to life in prison while his six sailors received ten years imprisonment. All the Salvador Pirates received commuted sentences from Andrew Johnson between December 1865 and May 1866 and went free.

So, there you have it. The famed Alcatraz prison, only a mere fort during the Civil War, actually was used as a prison then as well … at least ever so briefly with a handful of Confederate sailors and sympathizers. If you are ever in San Francisco, be sure to check out the island tour, cross the Golden Gate to get a good view of the city, and check out all the sights.


If you want to learn more about the activity along the Panamá route and its impact on the Civil War, be sure to check out my upcoming book Treasure and Empire in the Civil War: The Panamá Route, the West and the Campaigns to Control America’s Mineral Wealth, set for release in late 2023.


Stay tuned for the next Civil War stop in my travels through Utah, Nevada, California, and Oregon. Next stop: Fort Bragg, California!



[1] Louis Rossi, Six Years on the West Coast, 1856-1862, W. Victor Wortley, Trans., (Fairfield, WA: Ye Galleon Press, 1983), 72; Francis P. Farquhar, ed., Up and Down California in 1860-1864: The Journal of William H. Brewster, Professor of Agriculture in the Sheffield Scientific School from 1864 to 1903, (New Haven CT, Yale University Press, 1930), 9

[2] L.S.B. Sawyer, ed., Proceeds of the Schooner Chapman, January 13, 1864, Report of Cases Decided in the Circuit and District Courts of the United States for the Ninth Circuit, (San Francisco, A.L. Bancroft and Company, 1878), Vol. 4, 502.

[3] James H. Wilkins, ed., The Great Diamond Hoax and other Stirring Incidents in the life of Asbury Harpending, (San Francisco, CA: James H. Barry Co., 1913), 80.

[4] Ibid, 81.

[5] Sawyer, UNITED STATES V. GREATHOUSE ET AL., October 17, 1863, Report of Cases Decided in the Circuit and District Courts of the United States for the Ninth Circuit, Vol. 4, 458.

[6] Seward to Welles, January 19, 1865, Official Records of the Union and Confederate Navies in the War of the Rebellion, Series 1, Vol. 3, 368.

[7] Christine Reh Wyse, “William L. Black and the Southwestern Livestock Industry,” Master’s Thesis, Texas Tech University, August 1995, 11.

[8] General Order 52, June 27, 1865, The War of the Rebellion: The Official Records of the Union and Confederate Armies, Series 2, Vol. 8, 676-677.

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