England's test captain Root will play for Nottingham-based Trent Rockets, while Bairstow was picked up by Welsh Fire in Cardiff.
England's Ben Stokes will play for Northern Superchargers in The Hundred, with the Leeds-based franchise snapping up all-rounder ahead of Yorkshire pair Joe Root and Jonny Bairstow in the opening player picks for next year's new competition.
The new 100-ball format tournament was launched on Thursday, with eight new city-based teams officially named and the first batch of players allocated, including England's red-ball contracted players.
England's test captain Root will play for Nottingham-based Trent Rockets, while Bairstow was picked up by Welsh Fire in Cardiff.
The geographical element to the draft meant Stokes was only eligible for the Superchargers - who could pick Yorkshire and Durham players - and when coach Darren Lehmann opted for the World Cup-winning all-rounder, the Rockets chose Root over seamer Stuart Broad.
"Obviously I have been associated with Yorkshire and that part of the world for a long period of time, it'll always be home to me," Root told BBC Sport.
"But I have big connections with Nottingham too - my dad played there as a Colt and in the junior teams and second team and I've always loved playing there too.
"It's a great venue to be involved in - the wicket there is fantastic, there are nice, small boundaries so it's come together nicely in many ways."
England fast bowler Jofra Archer will represent Southampton-based Southern Brave, while Sam Curran joins his brother Tom at Oval Invincibles. England's leading test wicket-taker James Anderson and Broad were not chosen.
World Cup-winning captain Eoin Morgan was picked by London Spirit, all-rounder Moeen Ali joined Birmingham Phoenix and Jos Buttler will play for Manchester Originals.
The remaining places in the 15-man squads will be filled via a full draft on Oct. 20, with West Indies opener Chris Gayle and former Australia captain Steve Smith among those who have made themselves available for the tournament.
The eight women's teams have signed two players each from the 21 who are centrally contracted to England.
The women's competition will run alongside the men's under the same team names, with England captain Heather Knight representing London Spirit, while Professional Cricketers' Association women's player of the year Sophie Ecclestone will play for Manchester Originals.
The tournament will be played during the English summer starting July 2020. Teams will play each other once, apart from their paired 'rivals', whom they meet twice - home and away. There will be a total of 32 league matches, with the top three competing in the Finals Day.
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