In an announcement on social media, Murphy, a Democrat, said "The Confederate symbol does not reflect New Jersey’s values of inclusivity and equality."
He went on to thank state Sen. Sandra B. Cunningham (D-31) for her "leadership in bringing this forward."
The Mississippi flag will be replaced by the United States flag, Murphy also said.
The flags of all 50 states are flown annually from now until the fall at the park near the Statue of Liberty. Mississippi's flag is the only one that incorporates the Confederate symbol, also known as the Beauregard Battle Flag, which has come to represent the Southern states that seceded during the Civil War over the issue of slavery.
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