Forty-nine years after he allegedly raped a 16-year-old girl, a man is facing court after the son conceived that night tracked down his mother and encouraged her to go to police.

Moama man John Thomas O'Connell, now 69, has pleaded not guilty to a rape he was only recently charged with after the son born from the alleged assault was reunited with his mother.

John O'Connell has pleaded not guilty to the rape of a 16-year-old girl in 1967. Credit:Darren Howe/Bendigo Advertiser

Prosecutor Tim Hoare, in his opening to the jury in the Bendigo County Court on Wednesday, said the son was 33 when he found his birth mother in 2000 and she told him how he was conceived.

The son, who was given up for adoption when he was six months old, encouraged her to report it to police, Mr Hoare said. The report sparked an investigation in 2013-2014, which led to DNA being taken from Mr O'Connell, the son and his mother.