Miss Manning's partially naked body was discovered floating in the Avon River the day after she was killed.
ESR forensic scientist Jayshree Patel told the jury of six men and six women today that a knife found on the murky riverbed had her DNA on it.
It was 110 times more likely to have come from her than anyone else, Dr Patel said.
Other swabs taken from her body found DNA linked to two different men - an unknown male, known as 'male b', and a client she entertained on the night she died.
The trial, before Justice David Gendall, continues.
It will hear from more than 100 witnesses and is set down for another five weeks.
In his first police interviews, Fawcett described how Miss Manning was taken to the gang pad at Galbraith Avenue, Avonside, where she was raped, bashed and stabbed.
Fawcett initially told police that Mongrel Mob gangsters barked like dogs and gave Nazi salutes as they carried out the fatal assault. She was then dumped in the river 200 metres away.
Fawcett later backtracked from his earlier version of events, saying he wasn't present during the attack.
