The formation of the Alliance Premier League in 1979 was the first true attempt at a formation of a national league below the Football League. Twenty teams competed in the inaugural season, being drawn from the Northern Premier League and the Southern League. After 25 years, only Northwich Victoria remain as ever-presents, and they were demoted in 2005 to the Northern Division due to wranglings about the ownership of their new ground.

A major breakthrough in the Conference's history came in 1986 when the Football League finally agreed to automatic promotion and relegation. Scarborough were the first club to take advantage, replacing Lincoln City in Football League Division Four for 1987-88. From the 2002-03 season, a second promotion place was achieved, going to the winners of a play-off competition between those clubs in 2nd - 5th place.

Conference clubs have accounted for numerous Football League clubs in F.A. Cup ties over the years, with the biggest achievements have been of defeats of Division One (pre-Premiership days) clubs Birmingham City (by Altrincham), and Coventry City (by Sutton United). The furthest reached in the competition is the fifth round (i.e. the last 16), by both Telford United (1984-85) and Kidderminster Harriers in 1993-94.

A second layer, with Northern and Southern Divisions feeding into the existing league (re-christened as the National Division) started in 2004-05, heading the wholescale re-organisation of the non-league pyramid.

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                             Football League "League 2"
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                               Football Conference
                                National Division
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                 |                                                  |
         Football Conference                                Football Conference
          Northern Division                                  Southern Division
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             |                          |                                |
        Isthmian League        Northern Premier League           Southern League
        Premier Division         Premier Division                Premier Division

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