Gregory Gibbs, the temple's resident minister, said one of two pride flags on display at the temple's fence was torched Monday night.
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The temple didn't realize their rainbow flag was burned until Tuesday morning. A neighbor spotted the fire just after 7 p.m. Monday and doused the blaze with a garden hose, Gibbs said, but the neighbor didn't see who set the fire.
Pasadena police are investigating the flag burning as a possible hate crime.
Gibbs said the hand-painted flags have been on display for years and up until two weeks ago, no one had ever complained about them.
That changed earlier this month on April 6 when Gibbs said a man came in and complained about both flags.
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The temple refused to take the flags down. Surveillance video of the unidentified man was shared with police.
"This is our fundamental commitment to nondiscrimination," Gibbs said. "The Buddhist religion has never discriminated against people due to their race, their gender, their gender identity or their sexual behavior."
A Black Lives Matter flag and a similar rainbow flag now hang outside the temple, but Gibbs said they will look to replace the one that was burned.