The Hundred: Team-by-team guide and format
The new 100-ball tournament was launched on Thursday, with the eight franchises officially named and the first batch of players allocated, including England's centrally-contracted Test contingent.
The Headingley side, which represents Yorkshire and Durham, had an embarrassment of riches to choose from but could not look past Stokes, the undisputed star of the summer.
Test captain Root was picked up by Nottingham-based Trent Rockets instead, with Bairstow joining Welsh Fire in Cardiff.
Elsewhere Jofra Archer will spearhead the Southern Brave bowling attack, Jos Buttler heads up Manchester Originals, Chris Woakes represents Birmingham Phoenix and Sam Curran joins brother Tom at Oval Invincibles.
Each team was also able to pick up two 'icon' players from their local area, as well as the first two representatives of their women's side.
World Cup-winning captain Eoin Morgan is the leading man for the Lord's franchise, London Spirit, with England Women's captain Heather Knight also heading to the home of cricket.
Speaking about his new assignment Root said: "I'm incredibly excited to play for Trent Rockets in The Hundred.
"The best players in the world are coming here to compete and we're going to get the chance to test ourselves against them once again. There has never been a more exciting time for cricket.''
Bairstow welcomed the chance to represent Welsh Fire, even though returning to Yorkshire in the opposition ranks might take some getting used to.
"I enjoy Cardiff, I made my England debut there and it's an amazing place," he said.
"It's a new competition, a new format and new teams. It will feel weird going to Headingley and being in the away dressing room, but it's an amazing honour to be one of the guys to figurehead a team."
Hundred allocations
Birmingham Phoenix: Chris Woakes, Moeen Ali, Pat Brown, Amy Jones, Kirstie Gordon
London Spirit: Rory Burns, Dan Lawrence, Eoin Morgan, Heather Knight, Freya Davies
Manchester Originals: Jos Buttler: Saqid Mahmood, Matt Parkinson, Kate Cross, Sophie Ecclestone
Northern Superchargers: Ben Stokes, Adil Rashid, David Willey, Lauren Winfield, Linsey Smith
Oval Invincibles: Sam Curran, Tom Curran, Jason Roy, Laura Marsh, Fran Wilson
Southern Brave: Jofra Archer, Chris Jordan, James Vince, Anya Shrubsole, Danni Wyatt
Trent Rockets: Joe Root, Harry Gurney, Alex Hales, Nat Sciver, Katherine Brunt
Welsh Fire: Jonny Bairstow, Tom Banton, Colin Ingram, Katie George, Bryony Smith.
