Circuit Judge Luis Garcia ruled in favor of Aaron Huntsman and William Lee Jones in a lawsuit against the Monroe County clerk. A similar lawsuit is pending in Miami-Dade County. Garcia set Tuesday as a deadline.
Garcia said an amendment to the Florida Constitution, passed by 62 percent of the voters in 2008, violates the Equal Protection clause of the U.S. Constitution.
"The court is aware that the majority of voters oppose same-sex marriage, but it is our country's proud history to protect the rights of the individual, the rights of the unpopular and rights of the powerless, even at the cost of offending the majority," the judge wrote.
Most Monroe County residents live in the Keys, although the county includes Everglades National Park and Big Cypress National Preserve on the mainland. The county seat, Key West, has long been a center of gay life and hosts a seven-day PrideFest in June.
Assistant Attorney General Adam Tanenbaum argued at hearings in Monroe and Miami-Dade counties that the 2008 vote and a 1972 U.S. Supreme Court ruling that states have the authority to make laws on marriage have settled the issue.
"It remains for this court simply to respect the policy decision made by voters," Tanenbaum told Garcia at a July 7 hearing.
Matthew Staver of Liberty Counsel, a conservative group allowed to enter the case as a friend of the court, has accused Tanenbaum and Florida Attorney General Pam Bondi of "giving only window dressing to the Florida Marriage Amendment."
Federal and state judges across the country have recently struck down laws banning same-sex marriage. In Pennsylvania and Oregon, state officials have declined to appeal, but most other rulings have been stayed.