A three-year contract has been signed which will see the end of Nationwide's nine-year partnership with the three Conference leagues.
The Conference will be known as Blue Square Premier from next season, while the Conference North and South will be known as the Blue Square Northern and Blue Square Southern.
Football Conference chief Bill King told the BBC, "Our league is the gateway to the clubs in the professional structure in the UK and is an established part of the UK football scene.
"I'm delighted to be seeing a piece of non-league football history in the making and am extremely excited about what this partnership with Blue Square can achieve."