The first operational lighthouse on the west coast was built on Alcatraz. In the 1850s, the first military prisoners came to the island; most of them were soldiers who had to serve a short-term sentence for desertion or a lesser crime; some were serving longer sentences for insubordination, assault, larceny and murder. This initiated a change of role for Alcatraz which lasted until 1909, when the US Army destroyed the citadel, leaving only the basement as a foundation for a new military prison. The cannons on Alcatraz had never been fired in battle. It was the military prisoners on Alcatraz who had to build their own prison. It took them from 1909 to 1911 to build the 'Pacific Branch, US Disciplinary Barracks' for the US Army. 

In 1933, after more than 80 years of military use, control of Alcatraz was transferred to the US Department of Justice. The federal government wanted to make clear that it was serious about stopping the crime boom of the 1920s and 1930s. So a maximum-security and minimum-privilege penitentiary was installed on Alcatraz, which was now infamously known as 'the Rock'. The most dangerous and most incorrigible inmates in federal prisons were sent to the Rock.

Despite the intentions of the Federal Bureau of Prisons, living conditions on Alcatraz were better than in many other federal prisons. All the inmates had single cells and the food wasn't too bad either. The average population was about 270 inmates, but the prison had space for 336 men. Alcatraz never ran at full capacity. 

On 21 March, 1963, the US Prison Alcatraz was closed due to the enormous costs of operating a prison on an island. As there were absolutely no natural resources, everything from water (1 million gallons a week) to food and fuel had to be shipped there by boat. For six years, the island was abandoned. 

In 1969, a group of Native American Indians claimed Alcatraz as Indian land.   They had plans to create a Native American cultural centre. This act of civil disobedience was very popular among the anti-Vietnam war protesting scene in the late 1960s, so various celebrities, hippies, Hells Angels, and lots of other 'professional protesters' came to the island over the next 18 months. The situation could no longer be controlled by the Indians, and the island had to be cleared by the Federal Marshals in 1971 to prevent further vandalism. 

In 1972, the Golden Gate Recreational Area was created and Alcatraz was made part of it. It was opened to the public in 1973 and has been one of the most popular Park Service sites since then, with more than one million of visitors each year.