In this restless period, the Bohemian estates elected a new sovereign. Out of several candidates, they chose a member of a powerful family – the Hapsburg Ferdinand I (1526–1564), who was the husband of Anna Jagiellon. Even he had to sign an electoral capitulation in which he undertook to uphold and respect the privileges of the estates.
In the 16th century, the Hapsburgs not only controlled Central Europe, but Ferdinand’s brother Charles ruled in Spain from 1516, which had grown rich from extensive overseas colonies. In 1519, Charles was elected as king of Rome and he was made emperor in 1530. With the accession of Ferdinand Hapsburg, the Czech lands became part of a large combined state, which, besides them, principally comprised Austria and Hungary as well.
The Czech lands continued to participate in major international politics. However, unlike the preceding periods, they did not do so as the originator of these politics but as part of a greater whole. With a few short-lived exceptions, the sovereign’s court moved permanently to Vienna from Prague, which led to a decline in its significance.
As defenders of the Catholic faith, the Hapsburgs focused on religious wars with Protestants. At the same time as war was being waged in the empire, the Bohemian estates also revolted against Ferdinand in the years 1546–1547. The uprising, however, was not supported by the countries adjacent to the Bohemian state, and the fate of the resistance was decided following the defeat of its main ally, the Duke of Saxony. The royal cities were punished the most.
Religious wars in the empire did not end with the victory of the Catholic side. By entrenching the principle of “cuis regio, eius religio” (“Whose region it is, his religion it is”), the Peace of Augsburg in 1555 legalised the profession of a protestant faith. Religion was governed by the faith of the ruler, and the population had to follow him in this faith. This signified a defeat for the Hapsburgs, who had fought for a Catholic empire.
In 1556, Charles V stood down and Ferdinand I became the emperor. The Peace of Augsburg did not apply in the kingdom of Bohemia, however. Besides the Compactata of permitted Catholic and Ultraquist churches, Lutherans and Czech Brethren also operated illegally within the kingdom.
The Catholic Church did not intend to reconcile itself to losing its influence in Europe. At the Council of Trent, it declared its goal of re-Catholicisation and the restoration of its status. In 1561, the post of Archbishop of Prague was occupied for the first time since the Hussite era by Brus of Mohelnice. Czech Lutherans, Ultraquists, and the Bohemian Brethren agreed on a profession of faith in the so-called Bohemian Confession. This was supposed to ensure religious freedom and allow non-Catholic churches to have their own administration. In 1575, they submitted this to Maxmilian II (1564–1576). The sovereign did not have much room for manoeuvre in a situation where he needed the state assembly to approve a new tax and the election of his son Rudolph as King of Bohemia. Despite this, he only acknowledged the Bohemian Confession verbally without it being binding, but he never confirmed it in writing. The assembly sanctioned his requests.
By relocating the court from Vienna to Prague Emperor Rudolph II. (1576–1611) returned the lustre to Prague for a time as well as its importance as a capital city. Bohemia became the centre of his empire. Rudolph became renowned primarily as a patron, collector, and sponsor of astronomy, alchemy and astrology. But he was also known as an eccentric, who alternated between fits of madness and deep apathy.
Rudolph’s empire was under threat from the Turks. Hungarian magnates exploited this situation and entered into an alliance with them against the Hapsburgs. After one of the defeats that followed, the Hungarians won religious and political freedom through the Treaty of Vienna. Despite the fact that Rudolph was defeated, he refused to sign the treaty or to recognize its validity. Eventually, this was done by his brother the Emperor Matthias. The sickly Rudolph systematically suspected his brother of angling for the throne, and this is what eventually happened.
By boycotting the Treaty of Vienna, Rudolf set Matthias as well as the Hungarian, Austrian and Moravian estates against himself. They all rebelled against him in 1608. However, the Bohemian estates’ representatives did not rise up on the side of the rebels and Matthias had to come to an agreement with his brother. Rudolph II was forced to recognize the Peace of Vienna and to surrender the government of Hungary, Moravia and the Austrian lands to Matthias. He was left with Bohemia, Upper and Lower Lusatia. The Bohemian estates skilfully exploited the very weak position of the monarch and threatened him with the outbreak of a rebellion.
On 9 July 1609, Rudolf II preferred to issue his famous Rudolphine Letter of Majesty, in which he stated that nobody could be forced into Catholicism or any other faith. He confirmed the Bohemian Confession of 1575 and made reference to the nobility, the royal cities and serfs. He guaranteed freedom of religion regardless of the status of the individual. Thirty defenders of the faith were elected, comprising ten from each estate – the nobility, knights and the cities.
In an effort to exclude his hated brother from succeeding him, the dissatisfied Rudolph attempted to reverse the situation. He used the assistance of his relative, the Bishop of Passau, and let Passau forces invade Bohemia. Of course, this only gave rise to disapproval and outrage in the country. He was forced to also vacate the Bohemian throne, which was occupied by Matthias (who reigned from 1611 to 1619).