International swimming circles are shocked by the posting of the photos.
They are understood to have been taken in intimate moments during the glamorous Olympic and world championship gold medallist's relationship with 21-year-old Marin.
He has denied the accusations that he posted the photos as revenge for Manaudou dumping him.
They are understood to have broken up at the recent European short-course championships in Hungary.
THREW RING AWAY
Manaudou, who took gold in the 100m backstroke and 400 metres freestyle in Debrecen, threw away a ring given to her by Marin before arguing with him in front of other swimmers and the camera in the changing rooms on Sunday.
And in the hours following the row - and when it was also revealed that the Frenchwoman is now linked romantically to champion backstroker Benjamin Stasiulis of France - nude photos and a video of Manaudou appeared on the Internet.
Marin told Gazzetta dello Sport publication: 'I know nothing about the video and have only seen the photos.
'Yes, it looks like it's really her, but it is ridiculous to think that it was me who put them there.'
Marin, who lost his 400m European medley title to Hungary's Laszlo Cseh last Friday, also denied accusations from French witnesses that he had verbally abused Manaudou in public.
'They are inventions.
'I only said that she had done a very rude thing (by throwing the ring away) and that I was happy she was no longer my girlfriend,' he said.
Manaudou caused an uproar in France in May when she joined the LaPresse Nuoto club in Turin, Italy, saying she wanted a new challenge and wished to be nearer her then boyfriend Marin.
They even talked of having babies together.
But the club fired her three months later, citing attitude problems.
The love affair of Manaudou and Marin had captivated Melbourne during this year's world championships as photographers captured them frolicking together daily - kissing and hugging poolside.
They were the golden couple in swimming circles: She was a 2004 Athens Olympic gold medallist, she set world records to win in Melbourne in her freestyle events.
He was also a medallist in Melbourne in his chosen medley field.
In Manaudou's only public comments so far, she said: 'I've decided not to talk about my personal life anymore, it doesn't concern journalists.
'I would prefer to keep silent about this point.' --Reuters.