Republican candidate for the U.S. Senate in Alabama, Roy Moore, speaks at a campaign rally on September 25, 2017 in Fairhope, Alabama.

His decision likely makes it harder for Republicans to hold their 53-47 Senate majority. Jones seeks a full term in the Senate after his election to replace Jeff Sessions, who left the Senate in 2017 to become Trump's first attorney general.

"Yes, I will run for the United States Senate in 2020," Moore told reporters in Montgomery, Alabama, on Thursday, after questioning whether opponents lined up against him because he is a "staunch conservative" who believes in God.

Moore's entry into the 2020 race is worrisome for the GOP, which sees the race as its best chance to pick up a Senate seat next year. The former state Supreme Court chief justice lost a 2017 special election to Democratic Sen. Doug Jones despite Alabama's deep red hue.

Roy Moore, the former judge accused of sexual misconduct with teens decades ago, will run for U.S. Senate again in Alabama — defying the wishes of President Donald Trump and the Republican Party.

On Thursday, Moore claimed the 2017 election was "fraudulent" and left Alabama voters "tired" of "dirty politics." The Alabama secretary of State's office did not immediately respond to a request to comment on whether any evidence backed Moore's accusation that a disinformation campaign cost him the 2017 election.

Moore said "the people of Alabama are not only angry, but they're going to act on that anger."

During the Senate special election, the former judge denied several allegations that he made inappropriate advances on teens when he was in his 30s. On Thursday, he again called them "false claims" and "false information."

The Senate Republican campaign arm has distanced itself from Moore. Even Trump — who backed the ex-judge in 2017 as he ran a pro-Trump campaign — urged him not to run for Senate again. Trump endorsed him against Jones in 2017.

In a tweet last month, the president argued that "Roy Moore cannot win, and the consequences will be devastating." On Thursday, Moore denied that he had acted against the president's wishes.

"I'm not going against President Trump at all. I support President Trump," he said, adding that he thinks Trump is "being pushed" by the Senate Republican campaign arm.

National Republican groups warned that Moore's entry into the race could derail the GOP's efforts to win the seat.

In a statement Thursday, the Senate Leadership Fund — a super PAC aligned with Senate Majority Leader Mitch McConnell — said "we believe most Alabama Republicans realize that nominating Roy Moore would be gift wrapping this Senate seat for [Senate Minority Leader] Chuck Schumer." The National Republican Senatorial Committee pointed CNBC to a statement made last month by its chairman, Sen. Todd Young of Indiana.

"The people of Alabama rejected Roy Moore not too long ago," he told the AP at the time. "I with my Republican colleagues always want to be supportive of the most conservative candidate who can actually win a race, and I don't see that anything has changed in the state of Alabama since the last election."

Republican Rep. Bradley Byrne, the apparent mainstream GOP favorite, has jumped into the Republican primary. So has former college football coach Tommy Tuberville.

An early poll in April found Moore leading the Republican primary field with 27% of support. Still, much could change in the race before voters head to the polls in the spring.

In a statement, Byrne campaign manager Seth Morrow said, "Bradley is a fighter who has won contested primaries before." He added that "our campaign will win and defeat Doug Jones in 2020."

Jones' campaign tweeted that he would face either "extremist Roy Moore or an extremist handpicked by Mitch McConnell."

Doug Jones tweet: So it looks like my opponent will either be extremist Roy Moore or an extremist handpicked by Mitch McConnell to be part of his legislative graveyard team. Let's get to work so we can get things done!

Moore has faced punishment more than once for how he has interpreted the law based on his religious beliefs. He was suspended in 2003 for refusing a judge's order to remove a Ten Commandments monument from the state Supreme Court building.

Then in 2017, he lost an appeal to end another suspension after he argued Alabama should uphold its ban on same-sex marriage.

Moore ran unsuccessfully for statewide office before the 2017 election. He lost GOP gubernatorial primaries in both 2006 and 2010.

Asked Thursday what he would do differently to win in 2020, Moore said he would "like to make more personal contact with people."

— CNBC's Brian Schwartz contributed to this report.

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