Adam Scotti was photographing his boss at the Invictus Games over the weekend when Mr Trudeau grabbed the camera to snap a picture of the two redheads.
Mr Scotti then posted the image showing the uncanny resemblance on Twitter.
Prince Harry is in Toronto for the games and was sitting near Mr Trudeau and US First Lady Melania Trump during the opening ceremony.
The Canadian prime minister was not the only person to notice the striking resemblance between the shutterbug and the prince.
Another Twitter user posted a video of fans waiting to spot the prince outside a Toronto hotel, shouting "Harry!" when Mr Scotti walked through the doors.
Mr Trudeau, walking behind him, goes almost unnoticed until he jokingly points to his photographer and waves.
Mr Scotti kept having fun with the resemblance on Monday, posting an image of another Canadian photographer next to a portrait of Prince William.
He also joked about how he was waiting to be asked to play Harry in a biopic about the royal.
Mr Scotti has achieved a profile of his own in Canada even before people noticed he looked like Harry.
The young photographer has been called a "power player" in Canadian politics for helping craft Mr Trudeau's savvy social media image.
Prince Harry created the annual Invictus Games for wounded, injured and sick servicemen and women and veterans.
About 550 men and women athletes from 15 countries will compete over eight days.