As the ruler of Inner Austria he founded his own branch of the House of Habsburg, which was to become the main line of the dynasty in the following generation.
Charles’s powerful Spanish relatives played a considerable role in his search for a suitable wife. Negotiations were initiated for a marriage between him and Elisabeth I of England. In 1559 the Spanish court sent him to England, where he soon realized that his mission had no chance of success, as the Virgin Queen was not disposed to marry, and was most especially unlikely to consider a representative of a Catholic dynasty as a prospective husband.
Eventually his efforts to gain the hand of the Wittelsbach princess Maria of Bavaria (1551–1608) were crowned with success. She was the daughter of Duke Albrecht V of Bavaria and the Habsburg archduchess Anna (1528–1590), one of Charles’s aunts. He was thus marrying his first cousin. Brought up at the devoutly Catholic Munich court in the dogmatic Catholic tradition, Maria became a dominant figure in the Counter Reformation in the House of Habsburg.
Celebrated in 1571, the marriage produced fifteen children including six sons, of whom two died in infancy.
The extremely rapid succession of births is remarkable. After the wedding in August 1571 the first child was born in July 1572. This was a son named Ferdinand, who survived only a month. The following year in August saw the birth of a daughter, Anna, and a year later, in September 1574, of another daughter, Maria Christierna. She was followed by Katharina Renata in January 1576 and Elisabeth in March 1577, and in July 1578 the long-awaited son arrived, also called Ferdinand, who was to become emperor as Ferdinand II. Exactly a year later, in July 1579, another son named Karl was born, but died shortly afterwards. After an interval of barely two years Maria bore a daughter, Gregoria Maximiliane, in March 1581. After this births continued again at one-year intervals: in September 1582 Eleonore was born, to be followed in November 1583 by Maximilian Ernst and in December 1584 by Margarethe. After another pause of two years, in October 1586, Leopold was born, then Konstanze in December 1588, Maria Magdalena in October 1589, and finally Karl in August 1590. By the time Karl was born, his father had already been dead for several weeks. Maria thus bore fifteen children in eighteen years.