Police said two men walked into the store on 17th Street shortly before 9 p.m. as it was about to close.
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"Two suspects entered the store, one had a shotgun, they had their faces covered with bandanas, they ordered the clerk into the back room," said Cpl. Anthony Bertagna with the Santa Ana Police Department.
The clerk did not suffer any injuries, authorities said.
The thieves stuffed a bag with more than 40 cellphones while holding the clerk at gunpoint. Police said the two men took off in an awaiting car driven by a third suspect.
"Fortunately Duke was up, they were able to locate the vehicle, they followed the vehicle until they got off in the city of San Juan Capistrano," Bertagna said.
Duke, the Orange County Sheriff's Department helicopter, followed the car to Ortega Highway, where sheriff's deputies pulled it over. All three suspects were arrested.
Deputies found a shotgun and the phones in the car. The men booked for the robbery are: 21-year-old Andy Lopez of Riverside; 18-year-old Alex Perez of Chino; and 20-year-old David Martinez of Mira Loma.
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Police said cellphone store robberies like this are on the rise.
"Phones are expensive, and these suspects are taking the phones and selling them at swap meets, on the street," Bertagna said.
Santa Ana police are now checking with Los Angeles and Riverside counties to see if this crew might be linked to other similar crimes in the area.
Officers are crediting Duke's pilots for the arrests.
"Without them, in this particular case, we probably wouldn't have caught the suspects," Bertagna said.