The duchess Elizabeth moved to Austria, where she should live themselves in the future in the proximity of her husband, still imperial prissioner. The two young princes, Johann Casimir and Johann Ernst, moved to Coburg, the future residence of his new principality. With only six years, Johann Ernst was separated from his parents forever and entrusted to the education of strange persons. Since 1578 he visited the University of Leipzig then together with his brother. In 1586, after the wedding of his brother with Anna of Saxony, the daughter of the Elector Augustus, the guardianship finalized, and Johann Casimir began, together with his brother, the independent ruling of Saxe-Coburg-Eisenach. Johann Casimir and Johann Ernst governed together the principality for the next ten years; however, Johann Casimir carried the main responsibility for the government as an older brother. Also, in order to had a separated residence from his brother too, Johann Ernst establishes himself in the small town of Marksuhl on 1587. Since 1590 Johann Ernst withdrew himself from the government of the duchy, with his brother completely agreed it, that this should govern the duchy for five years alone, when this time had elapsed and finally agreed (in 1596) with its brother to a new divisionary treaty. The duchy of Saxe-Eisenach was taken by Johann Ernst as independent principality separated from Saxe-Coburg, who remained with Johann Casimir. Thus, Saxe-Eisenach, for the first time in his history, had his own independent political unit became within the Holy Roman Empire. During his first year of reign, Johann Ernst still live in Marsuhl because Eisenach, the new capital of his country, was inhabited and, only with the establishment of his official residence the citizens began to moved there. In 1598 Johann Ernst created for his duchy his own "Landesregierung" (State Government) and a "Konsistorium" (Consistory). In 1633 his brother, the duke Johann Casimir of Saxe-Coburg, died childless. For this, Johann Ernst inherited Saxe-Coburg, and until his own death he governed both countries in a personal union, but maintains, however, his residence in Eisenach. In Wiener Neustadt on 23 November 1591 Johann Ernst married firstly with Elisabeth of Mansfeld-Hinterort.