Yes, Alcatraz did have Dungeons

No, these are not relics of the Spanish days. At the time Henry Larry, Alvin Karpis, Joseph Bowers, and others spent time in these cells, they were barely 80 years old. These storage spaces from the old Citadel were used as cells both by the U.S. Army and by the Federal Bureau of Prisons until 1940 when renovations of the old D-Block and public opposition caused them to fall into disuse. The cells stood well-above the waterline. Reports of dampness may have been due to leakage from nearby fresh-water cisterns. The dark patches at the arched entryway shows where bars have been ripped out after the conversion of these areas into storage rooms.

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Photo by John Martini.
Courtesy Golden Gate National Recreation Area