The massive structure was found with ground-penetrating radar by researchers from Texas A&M.
The ruins are thought to be Fort Alcatraz, a long-forgotten military defense post located on the island.
The fort was supposed to be a first line of defense for Civil War troops looking to hold the Confederacy at bay.
Most of the findings will never be accessible but Texas A&M professor of geology and geophysics Mark Everett hopes to be able to explore at least one part. "It is called a caponier, and it is a large structure that juts out into the bay and provides defensive cover, " he began. “We have seen it in the old photographs, but it has completely disappeared from present view."
The fort was built long before the prison, "1850 to 1907 was the era of Fortress Alcatraz," Everett noted. It was completely buried when construction began on Alcatraz.
Among the discoveries thought to be inaccessible are tunnels, magazine buildings, and other fortified rooms.
Also discovered was what’s believed to be some of the oldest concrete in the history of our nation.
The fort didn’t see battle but there were several Confederate sympathizers held there during the war.
The Houston Chronicle reports the National Park Service is requesting a team to perform a thorough search for any structures that may be Civil War-related.