State Supreme Court Chief Justice Roy Moore, 69, potentially faces a hearing in front of a panel of judges, lawyers and other appointees.
Sanctions could include removing him from office.
The Judicial Inquiry Commission complaint said Moore had "flagrantly disregarded and abused his authority" in trying to block same-sex marriages, media reports said.
Moore responded that the commission had no authority over the matter, saying he would fight the charges and "expected to prevail."
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He accused the commission of listening to "people like (local transgender activist) Ambrosia Starling, a professed transvestite, and other gay, lesbian and bisexual individuals, as well as organisations which support their agenda."
Moore has repeatedly tried to stop same-sex marriage in Alabama. Last spring he told probate judges to ignore a federal court order striking down the state's ban on same-sex marriage.
In January, he ruled that Alabama's ban on same-sex marriages is legal and told probate judges there they had a "ministerial duty" to stop issuing licenses to gay couples.
The ruling came seven months after the US Supreme Court, in a historic 5-4 decision, held that states cannot prevent gay couples from marrying and that those that had refused to do so must now recognize such marriages.
"(Moore is) such a religious zealot, such an egomaniac that he thinks he doesn't have to follow federal court rulings he disagrees with.
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"For the good of the state, he should be kicked out of office," said Richard Cohen, president of the Southern Poverty Law Center, which filed a judicial ethics complaint that led to the Judicial Inquiry Commission action.
Most probate judges ignored Moore's orders, local media said.
Moore is known for his acts of resistance to federal authority.
He was removed as chief Alabama justice in November 2003 after refusing to give in to a judicial order to remove a monument bearing the Ten Commandments in front of the state Supreme Court.
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