Since the end of the Soviet Union, ROCOR has maintained its independence from the [[Church of Russia|Russian Orthodox ChurchPatriarchate of Moscow]] on the grounds that the Church inside Russia had been unacceptably compromised. Some accusations went so far as This was heightened when it came to claim light that the entire hierarchy many bishops and priests within Russia were active KGB agents. ROCOR also attempted to set up missions in post-Soviet Russia, which has not improved relations.

This has not prevented all communication, however. For many years there had been unofficial and warm contacts between the two groups. In 2001, the Synod of the Patriarchate of Moscow and ROCOR exchanged formal correspondence. The Muscovite letter held the position that previous and current separation was over purely political matters. ROCOR's response expressed concern over continued Muscovite involvement in [[ecumenism]], which was seen as compromising Moscow's Orthodoxy. Nevertheless, this was far more friendly discourse than had been seen previously.

After the dissolution of the Soviet Union, the Russian Orthodox Church Outside Russia continued to establish itself in its homeland. It now has about 100 worshiping communities in Russia and other countries of the Commonwealth of Independent States. Currently four bishops oversee these parishes. Two of them broke with Metropolitan [[Vitaly (Ustinov) of New York|Vitaly]] in New York in April 1994. They founded their own temporary administration called the ''Free Orthodox Church of Russia'' and ordained three additional bishops. They were reconciled in November 1994, and the ordination of the three new bishops was declared invalid. However, some tensions remain.