Rojas started with the department as a patrol officer in 1990 and rose through the ranks, becoming chief in May 2014.
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"For over 27 years, I have had the privilege and honor to serve the business owners, residents and all community members of this wonderful city," Rojas wrote in a memo announcing his resignation.
He said his last day would be June 9.
His resignation comes amid criticism from some elected officials over a recent rise in gang shootings and questions about the department's leadership.
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The Santa Ana Police Officers Association had announced plans for a "no confidence vote" against Rojas.
SAPOA president Gerry Serrano thanked Rojas for his service and called for the city to hire a new chief who can work on new strategies to make the city safer.
"Now we need a chief with a problem solving and community oriented policing strategy to address the spike in gang shootings and morale at the Santa Ana Police Department," Serrano said.