She was the daughter of Frederick II, Holy Roman Emperor, King of Sicily and Germany, by his third wife, Isabella of England.

Margaret was the daughter of Frederick II, Holy Roman Emperor, King of Sicily and Germany, by his third wife, Isabella of England.

Shortly after her birth (1242), Margaret was betrothed to Albert "the Degenerate", eldest son and heir of Henry III "the Illustrious", Margrave of Meissen.

The couple settled at his residence in Eckartsberga and later moved to Wartburg, where she bore five children: three sons (Henry, Frederick and Dietzmann) and two daughters (Margaret and Agnes).

In 1265 her husband received the titles of Landgrave of Thuringia and Count Palatine of Saxony (German: Pfalzgräf von Sachsen) after the abdication of his father, who retained control of Meissen.