Elvis Lorenzo Garcia, 21, of Santa Cruz, was arrested Friday at his workplace, a manufacturing business on Delaware Avenue.
He faces eight felony charges including kidnapping, robbery and sexual assault with enhancements, Santa Cruz County District Attorney Bob Lee said.
The arrest was the result of an investigation into the sexual assault of a 23-year-old barista at the Kind Grind coffee shop on East Cliff Drive on March 19, 2008.
The victim was an employee and was just opening the business when a man came inside, trapped her in the kitchen, held a knife to her throat and raped her, police said.
After assaulting and robbing the victim, the man tried to lock her in a freezer before fleeing on a bicycle.
Police now believe Garcia was the assailant. They said it does not appear he knew the victim, or had any contact with her prior to the attack.
Lee said the arrest could bring healing to residents shaken by the crime.
"When this case happened, it really left an open wound in our community because of the sheer randomness of the crime," Lee said.
As part of their investigation, Santa Cruz police detectives gathered evidence, developed a composite sketch of the suspect and loaded his profile into a DNA database, but no match was found.
After eight months, police requested help from the state Department of Justice to perform a familial DNA search, a process in which crime scene DNA is compared to the DNA of convicted offenders to see if there is a close match that could indicate a brother or father-son relationship.
In November 2010, the Department of Justice investigation identified two potential suspects in the case: Garcia and his father.
Police ruled out the father as a suspect and began tracking Garcia with the help of the Department of Justice and district attorney's inspectors.
They collected items from Garcia's trash such as a hair net and Gatorade bottle and compared them to the DNA sample from the 2008 sexual assault.
When they found a match, they obtained arrest and search warrants for Garcia. He is being held in Santa Cruz County Jail on $1 million bail.
He is expected to enter a plea on March 29. If convicted of all charges, he faces life in prison.