The period following the Thirty Years' War is often referred to as the "Dark Age" in Czech history, lasting from the mid-17th century until the late 18th century. This era was marked by the Habsburgs' consolidation of power and the systematic eradication of Protestantism, particularly Hussitism, which had thrived in the region prior to the war. The Habsburgs enforced strict Counter-Reformation measures, promoting Catholic orthodoxy while repressing dissent and limiting the rights of the largely Protestant Czech nobility.
In 1663, Moravia faced an invasion by Ottoman Turks and Tatars, leading to the capture of approximately 12,000 individuals as slaves. The Habsburg military responded under the command of Jean-Louis Raduit de Souches, achieving some success against the Ottomans by reclaiming territories like Nitra and Levice. A significant victory at the Battle of Saint Gotthard in 1664 forced the Ottomans to sign the Peace of Vasvár, which temporarily stabilized the region for about 20 years.
The reign of Leopold I (1656–1705) saw further military actions against the Ottomans, culminating in a successful campaign that restored parts of Hungary to Habsburg control. Following Leopold’s rule, Joseph I (1705–1711) and Charles VI (1711–1740) continued to navigate the complexities of Habsburg governance over diverse territories.
Under Emperor Charles VI, the Habsburg domains unified administratively in the early 18th century, establishing hereditary succession laws that allowed his daughter Maria Theresa to inherit the throne. The Habsburg-imposed unity across the Czech lands, however, continued to alienate the local nobility and the Czech-speaking population. For many Czechs, the repressive Counter-Reformation, economic decline, and the loss of a native Czech elite marked this era as one of hardship and cultural subjugation, setting the stage for later Czech nationalist movements​.
Despite the oppressive environment, the Baroque culture began to flourish in the Czech lands during this period and the era laid the groundwork for future social and educational reforms, and the eventual rise of the Czech national movement in the 19th century.