The group, led by Houston for Palestinian Liberation, was wearing red latex gloves to symbolize the tens of thousands of Palestinians killed in Israel's months-long bombardment of Gaza.
The demonstrators stood up at the beginning of Whitmire's keynote address Sunday evening at the Bayou City Event Center.
They unfurled a banner that read "No ceasefire, no iftar," as they chanted pro-Palestine slogans.
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According to ABC13's news partners at the Houston Chronicle, the demonstrators want the mayor to support a ceasefire in Gaza after his refusal to do so prompted some Muslim leaders and organizations to boycott the Iftar event.
Whitmire continued with his address, and the group continued to chant.
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"Hate is surrounding us, and the only way we're going to stop hate is not to let people divide us. We have to be united as Houstonians," Whitmire said.
The protesters were cleared from the room, and the night continued without further interruption.
Whitmire then said he would protect places of worship in support of Houston's Muslim community.
He added that he would "bring in other agencies, have random checks and prevention at our mosques."
A spokesperson confirmed with the Houston Chronicle that the mayor was referring to the Texas Department of Public Safety and other Houston-area law enforcement agencies.
"Houston Iftar" is observed by Muslims during Ramadan.