Salzburg originally was one of the biggest territories of the church in the HRE. But after Roman king Heinrich VIII started to annex clerical territories and the Twenty-Year War broke out, this time ended. The first years of the war, Salzburg stayed out, but then the Bavarian-Austrian War took place (1485-93). Finally they agreed that Bavaria could annex Salzburg, but had to give Eastern Styria in return to Austria.

But as soon as 1505-09, the Austrian-Seljuk War happened. The Rum-Seljuks invaded Austria, took Vienna, restricted the Austrian duke to mountainous Styria and Carinthia. And following that, they also defeated the Bavarian army, taking Salzburg and Bavaria east of the Inn river.

Salzburg was liberated again during the First French-Seljuk War 1567-74. In the Peace of Krems (Austria), the Seljuks had to cede Salzburg back to Bavaria and Austria to Württemberg-Carinthia, among others.

During 1578-1638, Salzburg was under the reign of Rupprecht VIII of Wittelsbach; after his death, it was reunited with Bavaria again.

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