Thirty-five-year-old Jorge Arellano of New Castle was arrested Monday during a traffic stop.
Troopers say Arellano confronted the woman at gunpoint in a Wilmington parking lot in January 2013.
Officers say he forced the woman into his car and touched her inappropriately while threatening her.
He eventually let her go, police said.
However, police say, while investigating that alleged crime, troopers learned of other incidents involving the same woman.
Arellano has been charged with nine counts of rape and numerous other offenses.
He is being held on $1.7 million cash bail.