Ivan IV was succeeded by his son Feodor, who was mentally deficient. Actual power went to Feodor's brother-in-law, the boyar Boris Godunov (who is credited with abolishing Yuri's Day, the only time of the year when serfs were free to move from one landowner to another). Perhaps the most important event of Feodor's reign was the proclamation of the Patriarchate of Moscow in 1589. The creation of the patriarchate climaxed the evolution of a separate and totally independent Russian Orthodox Church.

In 1598 Feodor died without an heir, ending the Rurik Dynasty. Boris Godunov then convened a Zemsky Sobor, a national assembly of boyars, church officials, and commoners, which proclaimed him tsar, although various boyar factions refused to recognize the decision. Widespread crop failures caused the Russian famine of 1601–1603, and during the ensuing discontent, a man emerged who claimed to be Tsarevich Demetrius, Ivan IV's son who had died in 1591. This pretender to the throne, who came to be known as False Dmitriy I, gained support in Poland and marched to Moscow, gathering followers among the boyars and other elements as he went. Historians speculate[44] that Godunov would have weathered this crisis had he not died in 1605. As a result, False Dmitriy I entered Moscow and was crowned tsar that year, following the murder of Tsar Feodor II, Godunov's son.

Subsequently, Russia entered a period of continuous chaos, known as The Time of Troubles (Смутное Время). Despite the Tsar's persecution of the boyars, the townspeople's dissatisfaction, and the gradual enserfment of the peasantry, efforts at restricting the power of the Tsar were only halfhearted. Finding no institutional alternative to the autocracy, discontented Russians rallied behind various pretenders to the throne. During that period, the goal of political activity was to gain influence over the sitting autocrat or to place one's own candidate on the throne. The boyars fought among themselves, the lower classes revolted blindly, and foreign armies occupied the Kremlin in Moscow, prompting many to accept Tsarist autocracy as a necessary means to restoring order and unity in Russia.

The Time of Troubles included a civil war in which a struggle over the throne was complicated by the machinations of rival boyar factions, the intervention of regional powers Poland and Sweden, and intense popular discontent, led by Ivan Bolotnikov. False Dmitriy I and his Polish garrison were overthrown, and a boyar, Vasily Shuysky, was proclaimed tsar in 1606. In his attempt to retain the throne, Shuysky allied himself with the Swedes, unleashing the Ingrian War with Sweden. False Dmitry II, allied with the Poles, appeared under the walls of Moscow and set up a mock court in the village of Tushino.

In 1609 Poland intervened into Russian affairs officially, captured Shuisky, and occupied the Kremlin. A group of Russian boyars signed in 1610 a treaty of peace, recognising Ladislaus IV of Poland, son of Polish king Sigismund III Vasa, as tsar. In 1611, False Dmitry III appeared in the Swedish-occupied territories, but was soon apprehended and executed. The Polish presence led to a patriotic revival among the Russians, and a volunteer army, financed by the Stroganov merchants and blessed by the Orthodox Church, was formed in Nizhny Novgorod and, led by Prince Dmitry Pozharsky and Kuzma Minin, drove the Poles out of the Kremlin. In 1613 a zemsky Sobor proclaimed the boyar Mikhail Romanov as tsar, beginning the 300-year reign of the Romanov family.