Otis Hughes is suspected of sexually assaulting, hogtying and killing 39-year-old Karen Wong on Feb. 27, 1991 inside her residence in the 400 block of 47th Avenue, police said.
Hughes, now 56, was taken into custody at his Hilltop Drive home in the city of Richmond on Tuesday evening, on a warrant issued by the San Francisco District Attorney's office, according to authorities.
Hughes was identified by DNA evidence obtained at the scene of the crime, police and the district attorney's office said.
"It's been nearly 20 years since this woman was raped, hogtied and stabbed to death in her own home, but our commitment to bringing her killer to justice has not wavered," District Attorney Kamala Harris said in a statement.
According to prosecutors, Hughes had been suspected of committing several residential burglaries in the 1980s and early 1990s.
Hughes was convicted of residential burglary in 1991, and served 17 years of a 34-year prison sentence, prosecutors said.
He was released in October and investigators were notified of the DNA hit later the same month, according to prosecutors.
Hughes is also facing a special circumstances allegation of murder committed during the course of a rape, prosecutors said. He is being held on $2 million bail and is scheduled to make an initial appearance in San Francisco Superior Court Friday morning.