Amid conflicting signals from federal courts and the chief justice of Alabama’s Supreme Court, some Alabama counties began granting marriage licenses to same-sex couples on Monday in a legal showdown with echoes of the battles over desegregation in the 1960s.

In major county seats like Birmingham, Montgomery and Huntsville, same-sex couples lined up outside courthouses as they opened and emerged smiling after being wed.

At the Jefferson County Courthouse here, Judge Michael G. Graffeo of Circuit Court officiated, at times tearfully, at the civil wedding of Dinah McCaryer and Olanda Smith, the first to emerge from the crowd of same-sex couples on Monday morning. “I now pronounce Olanda and Dinah are married spouses, entitled to all rights and privileges, as well as all responsibilities, afforded and placed upon them by the State of Alabama,” Judge Graffeo said.

But in 43 of Alabama’s 67 counties, the county Probate Courts, which issue the licenses, were not giving them to gay and lesbian couples, according to the Human Rights Campaign, a gay rights group. Many Probate Court judges declined to grant any marriage licenses.

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