A firefighter suffered minor injuries in the stubborn blaze, which was reported shortly after 4 a.m. at Good Shepherd Bible Church in the 6700 block of Washington Avenue.
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Nearby resident Genelle Melendez said she opened her back door "and all I could see was flames outside and I'm like, 'Oh, my gosh!'" She said she then ran to alert others about the fire.
Los Angeles County firefighters on aerial ladders attacked dramatic flames that shot through the roof of the sprawling single-story structure. Hours later, the fire was finally extinguished.
The structure was deemed a total loss.
Nevertheless, the head of the church vowed that a service will still be held on Sunday, even if the congregation has to gather in the parking lot.
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"I hate to see this beautiful building go - a historic place of Whittier," Pastor Samuel Gamboa said in an interview. "But we are the church and the church will continue."
Chief Anthony Whittle of the Los Angeles County Fire Department sought to reassure residents about the agency's resources amid extreme red flag conditions.
The department "has been at full capacity for the last few days because of the weather," Whittle said. "But what you see here today is a typical second-alarm fire for our department and we were not strained."
The cause of the blaze, which originated in the building's attic, was not immediately known.
"I'm so saddened," Gamboa, the pastor, said. "But my faith is that God has a plan for us."