The city of San Francisco confirmed it had removed the "Appeal to Heaven" flag from outside City Hall over the weekend, just days after it was reported to have been flown outside a conservative Supreme Court justice's house.

On May 22, the New York Times reported Supreme Court Justice Samuel Alito flew the Pine Tree flag at his New Jersey vacation home last year and described it as "a symbol of support for former President Donald J. Trump, for a religious strand of the ‘Stop the Steal’ campaign and for a push to remake American government in Christian terms."

The San Francisco Chronicle reported Wednesday that the Revolutionary War-era flag was taken down after 60 years in the Civic Center Plaza on Saturday. 

In a statement given to the Chronicle, city parks officials said they removed the flag because while it first symbolized the "quest for American independence," it has "since been adopted by a different group — one that doesn’t represent the city’s values."

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Appeal to Heaven flag

The city of San Francisco removed the "Appeal to Heaven" flag from near City Hall because of its association with anti-democratic groups. (SOPA Images / Contributor)

The Chronicle explained the Pine Tree flag’s history as a patriotic symbol, stating it was "originally flown from George Washington’s ships during the Revolutionary War." However, it also claimed the meaning of the flag has changed in the modern context.

"It’s among several images appropriated by conservative movements and appeared conspicuously in riots at the U.S. Capitol on Jan. 6, 2021, carried by people seeking to stop the certification of Joe Biden’s election as president," The Chronicle reported.

The outlet reported that the Appeal to Heaven flag "was among the original 18 raised by the city on June 14 — Flag Day — in 1964." According to a city parks statement to The Chronicle, each flag flown commemorates "a key moment in or symbol in American history," including the Gasden flag and Texas Lone Star state flag. 

The statement noted city officials had removed another controversial flag in the past - the Confederate flag in 1964.

Critics rebutted the attempt to discredit Alito by calling the flag a Jan. 6 symbol to link him to the movement.

"This is just one of many historic American flags out there. And they're trying to parlay it, through some kind of, you know, conspiracy theorist guilt by association thing into somehow he's supporting insurrectionists or something," Judicial Crisis Network President Carrie Severino told Fox News Digital

The City Hall in San Francisco

The City Hall in San Francisco, Calif. on Friday, June 7, 2019. (Photo by Paul Chinn/San Francisco Chronicle via Getty Images)

Former Vice President Mike Pence, who was in the Capitol on Jan. 6 and a possible target of the crowd, said, "The controversy over Justice Alito flying the ‘Appeal to Heaven’ flag is absurd and anti-historical. The flag was commissioned by George Washington in 1775 for use on six cruiser ships intercepting British vessels at sea and became the maritime flag of Massachusetts."

"The flag draws its meaning from John Locke," he added, following up with a quote from the famous thinker: "’And where the Body of the People, or any single Man, is deprived of their Right, or is under the Exercise of a power without right, and have no Appeal on Earth, then they have a liberty to appeal to Heaven, whenever they judge the Cause of sufficient moment.’ The Second Treatise on Civil Government (1689), John Locke."

"The ‘Appeal to Heaven’ flag is part of our proud heritage of Faith and Freedom and every American should be proud to fly it," he concluded.

Associate Justice Samuel Alito

Liberal media and Democratic Party leaders have used the classic "Appeal to Heaven" colonial-era flag to link Supreme Court Justice Alito to Jan. 6 insurrectionists. (AP Photo/J. Scott Applewhite, File)

This was Alito’s second flag controversy in a matter of days, after The Times linked an "upside-down American flag" being flown at Alito’s Virginia home in the weeks after the Jan. 6 riot to support for "Stop the Steal" and the attack on the Capitol.

After some in the media attempted to smear Alito over his two flags, prominent Democratic Party members got in on the mix. Sen. Sheldon Whitehouse, D-R.I., said on X that Alito’s "Appeal to Heaven" flag was a "MAGA battle flag," in one instance.

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The Civic Center Plaza did not immediately respond to Fox News Digital's request for comment.

Fox News' Timothy H.J. Nerozzi contributed to this report.