The 1979–80 season was the 65th season of the Isthmian League, an English football competition.
At the end of the previous season Alliance Premier League was created. As a result of it, Isthmian League clubs lost possibility to take part in the elections to the Football League as only highest placed club from Alliance Premier League who met the Football League requirements may apply. Isthmian League refused to participate in the formation of the new league. There was no promotion from the Isthmian League to the Alliance Premier League till 1985.
Leytonstone also relegated from the Premier Division at the end of the previous season, merged with Ilford to create the new club Leytonstone & Ilford, thus, St Albans City were reprieved.