Sean Banks, 37, met the victim on the matchmaking website Christianmingle.com, where he went by the user name "Raritiy," La Mesa Police said in a statement.
Banks used three additional online identities -- "Rylan," "Rylan Butterwood" and "Rylan Harbough" -- and police said they are concerned "there may have been more cases with other women."
ChristianMingle touts a safety section that includes a warning to avoid contact with members who cannot take "no" for an answer.
The site is cooperating with the investigation, CNN affiliate KSWB reported.
Banks was arrested February 11 and has been booked on two rape charges in the incident as well as one count of residential burglary, police said.
He has pleaded not guilty and is free on his own recognizance after posting $500,000 bail.