The Spanish and Austrian Habsburg European lands, ca 1700
Charles formally became the sole monarch of Spain upon the death of his imprisoned mother Queen Joan in 1555.
After the abdication of Charles V in 1556, the Habsburg dynasty split into the branch of the Austrian (or German) Habsburgs, led by Ferdinand, and the branch of the Spanish Habsburgs, initially led by Charles's son Philip. Ferdinand I, King of Bohemia, Hungary, and archduke of Austria in the name of his brother Charles V became suo juremonarch as well as the Habsburg Holy Roman Emperor (designated as successor already in 1531). Philip became King of Spain and its colonial empire as Philip II, and ruler of the Habsburg domains in Italy and the Low Countries. The Spanish Habsburgs also ruled Portugal for a time, known there as the Philippine dynasty (1580–1640).
The Seventeen Provinces and the Duchy of Milanwere in personal union under the King of Spain but remained part of the Holy Roman Empire. Furthermore, the Spanish king had claims on Hungary and Bohemia. In the secret Oñate treaty of 29 July 1617, the Spanish and Austrian Habsburgs settled their mutual claims.
Austrian Absolutism: The Habsburg Empire 1765-1790
The Habsburgs sought to consolidate their power by frequent consanguineous marriages, resulting in a cumulatively deleterious effect on their gene pool. Health impairments due to inbreeding included epilepsy, insanity and early death. A study of 3,000 family members over 16 generations by the University of Santiago de Compostela suggests inbreeding may have played a role in their extinction. Numerous members of the family showed specific facial deformities: an enlarged lower jaw with an extended chin known as mandibular prognathism or 'Habsburg jaw', a large nose with hump and hanging tip ('Habsburg nose') and an everted lower lip ('Habsburg lip'). The last two are signs of maxillary deficiency. A 2019 study found that the degree of mandibular prognathism in the Habsburg family shows a statistically significant correlation with the degree of inbreeding. A correlation between maxillary deficiency and degree of inbreeding was also present but was not statistically significant. Other scientific studies, however, dispute the ideas of any linkage between fertility and consanguinity.
The gene pool eventually became so small that the last of the Spanish line, Charles II, who was severely disabled from birth (perhaps by genetic disorders), possessed a genome comparable to that of a child born to a brother and sister, as did his father, probably because of 'remote inbreeding'.
The death of Charles II of Spain in 1700 led to the War of the Spanish Succession and that of Emperor Charles VI in 1740 to the War of the Austrian Succession. The former was won by House of Bourbon, putting an end to Habsburg rule in Spain. The latter, however, was won by Maria Theresa and led to the succession of the House of Habsburg-Lorraine (German: Haus Habsburg-Lothringen) becoming the new main branch of the dynasty in the person of Maria Theresa's son, Joseph II. This new House was created by the marriage between Maria Theresa and Francis Stephan, Duke of Lorraine.
(Both of them were great-grandchildren of Habsburg emperor Ferdinand III, but from different empresses.) This new House was a cadet branch of the female line of the House of Habsburg and the male line of the House of Lorraine.