In Altenburg on 24 October 1636, Ernst married his cousin Elisabeth Sophie of Saxe-Altenburg. As a result of this marriage Saxe-Gotha and Saxe-Altenburg were unified, when the last duke of the line (Elisabeth's cousin) died childless in 1672. Ernst and Elisabeth Sophie had eighteen children: Johann Ernest (b. Weimar, 18 September 1638 – d.
Joseph, Duke of Saxe-Altenburg: 26. Charles II, Grand Duke of Mecklenburg-Strelitz (= 22) 13. Duchess Charlotte Georgine of Mecklenburg-Strelitz: 27. Princess Friederike of Hesse-Darmstadt (= 23) 3. Princess Alexandra of Saxe-Altenburg: 28. Frederick II Eugene, Duke of Württemberg (= 18) 14. Duke Louis of Württemberg: 29.