A San Pedro resident was charged Wednesday with murdering former Cal Poly San Luis Obispo classmate Kristin Smart during the commission of a rape or attempted rape, with the county’s top prosecutor there saying there may be other sexual assault victims in Southern California.

San Luis Obispo County District Attorney Dan Dow told reporters that the case against Paul Ruben Flores, now 44, mark a “major milestone” in an investigation that has involved three sheriffs and three district attorneys in that county over a nearly 25-year period.

The criminal complaint alleges that Smart was killed on May 25, 1996, while Flores was “engaged in the commission of, or attempting to commit, the crime of rape.”

“We certainly believe that Mr. Flores’ dorm room was the crime scene,” the prosecutor said, noting that the young woman was last seen alive “close to the dorms.”

Flores was the last person seen with the 19-year-old college freshman before she disappeared while on her way home from an off-campus party. Flores — also a 19-year-old college freshman at the time — was seen walking on a path to the college dormitories with her at about 2 a.m. that day, according to San Luis Obispo County Sheriff Ian Parkinson.

Her body has not been found.

Flores’ 80-year-old father, Ruben Ricardo Flores, is charged with being an accessory to the fact. He is accused of helping to conceal the 19-year-old woman’s body after she was killed, according to Dow.

The two men are set to be arraigned Thursday in a San Luis Obispo County courtroom.

Prosecutors carefully reviewed the case and independently concluded that they have “enough evidence to go forward and prosecute both Mr. Paul Flores and Ruben Flores,” Dow said.

The district attorney noted that investigators are requesting information from the public “about this case or other potential crimes believed to have been perpetrated by Paul Ruben Flores, including assaults or other acts.”

“If you’ve been a victim in another location, perhaps in San Pedro, we want you to come forward to law enforcement so that you can get assistance that you need and it may help us in this particular case as well,” he said.

Investigators “do have evidence in this case that leads us to conclude that there very well may be additional victims in the Southern California area,” Dow said, noting that the younger Flores was “known to frequent bars in the San Pedro area starting in 2005.

“At this point we’re concerned about sexual assault,” he said, noting that the complaint includes a statement that the prosecution intends to use “evidence of other sexual crimes in this prosecution.”

“… So, based on that, I can tell you that we do believe that we have evidence, that we do believe that there are other people that are not yet identified that have had some kind of a criminal act perpetrated on them by Mr. Flores,” Dow added.

He declined to talk about how Smart was killed, saying that is something prosecutors will address in court.

The district attorney added that Smart’s family has been “incredibly gracious” over the years, saying they “willed this moment to happen.”

Flores, long described as a “prime suspect” by authorities, was taken into custody in San Pedro at about 7:30 a.m. Tuesday, while his father was simultaneously arrested in Arroyo Grande, where he lives.

Parkinson said investigators had served search warrants at the younger Flores’ home and simultaneously at the residences of his mother, father and sister, in February 2020, telling reporters Tuesday that “physical evidence recovered during these searches led to the service of (an) additional search warrant at Paul Flores’ residence in April last year.”

“During the search warrant, detectives recovered evidence related to the murder of Kristin Smart,” the sheriff said, adding that “additional evidence related to the Smart investigation” was discovered last month when a search warrant was served at Ruben Flores’ home.

A San Luis Obispo County judge subsequently signed arrest warrants for the father and son, along with two additional search warrants, the sheriff said during a news conference Tuesday afternoon at Cal Poly San Luis Obispo.

“We will continue to focus on finding her remains regardless of any court action,” Parkinson said. “We will continue the process of finding out where Kristin is. We know that’s an important part or important issue with the family.”

“… It’s my hope that we’re able to take the first step toward justice for the Smart family, peace for the community, some justice out there for all of us and most especially for Kristin,” the sheriff said. “I have spoken to the Smart family numerous times including this morning, matter of fact twice today. I think they’re feeling a bit of relief, but as you can imagine, until we return Kristin to them this is not over. And we have committed to them that we are not going to stop until Kristin has been recovered no matter what the cost, no matter what the time. We are committed to that. I know they believe in us. I know they believe we will find Kristin.”

In a statement released after the arrests, the Smart family said, “For over 24 years, we have waited for this bittersweet day. It is impossible to put into words what this day means for our family. We pray it is the first step to bringing our daughter home. While Kristin’s loving spirit will always live in our hearts, our life without her hugs, laughs and smiles is a heartache that never abates.

“The knowledge that a father and son, despite our desperate pleas for help, could have withheld this horrible secret for nearly 25 years, denying us the chance to lay our daughter to rest, is an unrelenting and unforgiving pain,” their statement says. “We now put our faith in the justice system and move forward, comforted in the knowledge that Kristin has been held in the hearts of so many and that she has not been forgotten … We are pleased that Kristin’s case has now moved to the district attorney’s office, where we know we will be in good hands, and look forward to the day when there will be justice for Kristin.”

Flores has lived for more than a decade in San Pedro, where authorities served a search warrant at his Upland Avenue home last April, looking for unspecified items of evidence related to the investigation into Smart’s disappearance.

In February 2020, search warrants were served in San Pedro, San Luis Obispo County and Washington state, but authorities declined to provide any specifics.

In 2016, federal investigators dug up a hillside near the Cal Poly San Luis Obispo campus, looking for remains. They also searched the yard of a home. Investigators also examined vehicles that Flores and his father owned at the time of Smart’s disappearance.

“Since I came into office in 2011, we have served over 41 search warrants on this case, done physical searches of 16 different locations …a complete re-examination of every physical item seized, submission of 37 items of evidence from the early days of the case for modern DNA testing, recovery of 193 items of physical evidence, new physical evidence,” the sheriff told reporters. ” We’ve conducted approximately 137 person-to-person interviews and in addition completed over 500 additional police reports.”

The investigation into Smart’s disappearance was initially handled by Cal Poly police, then turned over about a month later to the San Luis Obispo County Sheriff’s Office. The FBI, California Department of Justice and numerous law enforcement agencies have also provided assistance, Parkinson said.

Smart’s family has sued Flores in civil court. He invoked his 5th Amendment right against self-incrimination before a grand jury and in a civil deposition.

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