Until Monday, Chief Justice Roy S. Moore of Alabama had what some legal experts called a plausible argument for delaying the onset of same-sex marriage in the state, which had been ordered by a Federal District Court judge. After all, the United States Supreme Court will decide the issue for the entire nation in coming months and it made sense, Chief Justice Moore and other opponents of same-sex marriage said, to freeze things until the highest court ruled.

The argument may have been plausible, but it became irrelevant on Monday as the Supreme Court, with only two dissenters, said it would not grant the stay the state had sought.

On Monday, as some of the state’s probate judges began to issue marriage licenses to same-sex couples while many more still refused, a clash of federal and state authority began to unfold. But legal experts said it would almost surely end with state officials honoring the federal decision, which was issued last month by Judge Callie V. S. Granade of United States District Court.

Chief Justice Moore had raised the stakes on Sunday night, issuing a letter saying that probate judges should not “issue or recognize a marriage license that is inconsistent” with the state’s Constitution, which limits marriage to a man and a woman. On Monday, after the loss in the Supreme Court, he appeared to grasp at one more legal straw, arguing that the federal court order was not binding on the probate judges because it had been addressed to the state attorney general, and not its judiciary.