Paul Flores "continues to be a person of interest in the disappearance of Kristin Smart in 1996," the San Luis Obispo County Sheriff's Department said in a statement.
The Los Angeles County Sheriff's Department assisted in serving the search warrant, which remained sealed, the news release said. No other details were immediately disclosed.
News video from AIR7 HD showed investigators entering and exiting a single-story house in San Pedro.
September 2016: FBI renews search for Cal Poly San Luis Obispo student missing for 20 years
San Luis Obispo County authorities in February served search warrants at four locations in the states of California and Washington.
Smart was last seen returning to her California Polytechnic State University dormitory in San Luis Obispo from an off-campus party on May 25, 1996.