In Pasadena, the pastor of the 4,000-member All Saints Church spoke out against Proposition 8, calling the religious community's support of it "embarrassing."
Several other demonstrations were planned around the state.
In Orange County, about 1,000 gay-rights advocates fanned out along sidewalks leading to Saddleback Church in Lake Forest.
The protesters were angered by the church's support of Proposition 8, a constitutional amendment approved by voters Tuesday that bans same-sex marriages and overturns the state Supreme Court decision in May legalizing such unions.
Human Rights Campaign volunteer Ed Todeschini accused the church of helping propagate what he called misinformation about the Supreme Court ruling, including that gay marriage would have to be taught to kindergartners.
A message for comment left at the church's main office, which was closed Sunday, was not immediately returned.
"They told such obvious lies, they used their lies to deceive the public," Todeschini said of the church, which gained national attention in August when its pastor, Rick Warren, brought Obama and McCain together to discuss their religious faith. The two candidates embraced during what was otherwise an often-contentious presidential campaign.
Todeschini said Sunday's rally was peaceful, with demonstrators waving placards with slogans including "Equality for all" and "Shame on you."
Other demonstrations were planned across the state, including in San Francisco, Laguna Niguel, at a park in Los Angeles and outside a Mormon Temple in San Diego. Rallies have been taking place since Proposition 8's passage. It won with 52 percent of the vote.
In Oakland, where the highway patrol rerouted traffic, protest organizers said they hoped to tone down the anger that has characterized some previous protests.
"Our intent is not to disturb churchgoers," organizer Tim DeBenedictis said in a statement. "Our goal is to mend fences and build bridges so that all Californians can achieve marriage equality under the law."
Not all churches favor Proposition 8. In Pasadena, the All Saints Church announced that while it could legally no longer marry same-sex couples, it would continue blessings of gay civil unions.
"It's very unfortunate and embarrassing that the (Christian religion) is in large part responsible for this act of bigotry," the Rev. Ed Bacon told The Associated Press following his Sunday sermon.
Bacon heads the 4,000-member All Saints Church.
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