Sabrina by Nick Drnaso narrates the story of a girl who goes missing, leaving behind a videotape with clues about her disappearance.
Chicago-born Drnaso, who is 29, won an LA Times book prize with his first collection Beverly.
“Given the changing shape of fiction, it was only a matter of time before a graphic novel was included,” the judges said.
This year’s Man Booker Prize longlist consists of six writers from the UK, three from the US, two from Ireland and two from Canada.
The eligibility rules were changed in 2013 to allow international authors to be nominated, as long as their book was written in English and published in the UK.
The longlist for the £50,000 prize will be whittled down to six in September before the final winner is announced on Tuesday 16 October.