Vincent O'Sullivan, 55, was taken into custody Saturday in Guerneville.
O'Sullivan allegedly threatened to harm the LGBTQ community with explosives and twice stole a rainbow flag from the Guerneville Chamber of Commerce.
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The flag, symbolizing LGBTQ pride, was stolen on April 26 from the building at 16201 First Street in the unincorporated area of Guerneville in Sonoma County. Sonoma County sheriff's deputies began investigating the theft.
The building arranged for a replacement, but the flag was again stolen on May 5. According to Sonoma County's website, Guerneville became a "welcoming resort area for Bay Area gay men and lesbians" in the 1970's.
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During the investigation, deputies learnt of a suspect making threats to detonate a pipe bomb at the Guerneville Safeway.
Deputies said the suspect's intent was to injure deputies and members of the LGBTQ community.
He could face charges including making criminal threats, along with hate-crime enhancements.
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ABC7 News contributed to this story.