Parts of the domain were located in Denmark (in the Duchy of Schleswig), mainly on the islands of Als and Ærø and around Glücksburg, whilst other lands were part of the Holy Roman Empire (in the Duchy of Holstein), including the Ämter of Plön, Ahrensbök, and Reinfeld.
As a result of various inheritance arrangements it fragmented into numerous small territories which were eventually absorbed into Greater Denmark in the 18th century.
His domain included inter alia the territories of Sonderburg, Norburg, Ærø, Plön and Ahrensbök together with their assigned Ämter or administrative offices.
The dukes of Schleswig-Holstein-Sonderburg repeatedly split their possessions among their heirs, so that a variety of very small territories came into existence.
After the death of Duke John in 1622, the duchy was divided among those sons who were legal heirs and the House of Schleswig-Holstein-Sonderburg produced several collateral lines.