Yes, Margaret was an Archduchess. She was born Archduchess Margaret of Austria, a member of the House of Habsburg-Lorraine, the eldest daughter of Archduke Karl Ludwig of Austria and Princess Maria Anna of Saxony. She was married to Archduke Franz Ferdinand of Austria, heir apparent to the Austro-Hungarian throne.
The Remarkable Reign of Margaret of Austria: A Quiz on the Dowager Princess of Asturias