Subbotniks, meaning sabbatarians for their observance of the Sabbath on Saturday, as in the Old Testament, rather than on Sunday, arose as part of the Spiritual Christian movement in the 18th century. Imperial Russian officials and Orthodox clergy considered the Subbotniks to be heretical to Russian Orthodox religion, and tried to suppress their and other Judaizing sects, which adopted some Mosaic practices, such as circumcision of boys. They also emphasized individual interpretation of the law, rather than accepting the Talmud or clergy. The Subbotniks concealed their religious beliefs and rites from the Orthodox Christians. The Russian government eventually deported the Subbotniks, isolating them from Orthodox Christians and Jews.
The Subbotniks observed the Sabbath on Saturday, and were also known as sabbatarians. They avoided work and tried to avoid discussing worldly affairs. Apart from practicing circumcision of boys, many began to slaughter their food animals according to the laws of shechita when they could learn the necessary rules. Some clandestinely used tefillin, tzitzit, and mezuzot, and prayed in private houses of prayer. As their practice deepened, some acquired Jewish prayer-books with Russian translation for their prayers. The cantor read the prayers aloud, and the congregants prayed silently; during prayers a solemn silence was observed throughout the house.
According to the testimony, private and official, of all those who studied their mode of life in Czarist times, the Subbotniks were remarkably industrious; reading and writing, hospitable, not given to drunkenness, poverty, or prostitution. Up to 1820 the Subbotniks lived for the most part in the governments of Voronezh, Oryol, Moscow, Tula, and Saratov. After that year, the government deported those who openly acknowledged their membership in the sect to the foothills of the Caucasus, to Transcaucasia, and to the governments of Irkutsk, Tobolsk, and Yeniseisk, in Siberia. In 1912, the government Interior Ministry recorded 8,412 Subbotniks; 12,305 Judaizing Talmudists; and 4,092 Russian Karaites.
Under Alexander I's policies of general tolerance, the Subbotniks enjoyed a great deal of freedom. But the Russian clergy opposed them and killed about 100 Subbotniks and their spiritual leaders in Mogilev, in present-day Belarus, including the former archbishop Romantzov. In addition, Romantzov's young son was tortured with red-hot irons before being burned at the stake. The Subbotniks came to an agreement with the Russian Orthodox priests and succeeded in gaining a measure of peace for a period. To compensate the Church for any loss of finances due to the Subbotniks leaving their congregations, the members of the sect undertook to pay the Church the usual fee of two Russian rubles for every birth and three rubles for every marriage. The tsar permitted the Subbotniks to profess their faith openly, but prohibited them from hiring rabbis or proselytizing among Christians.
Under Nicholas I, the Subbotniks began to feel restless. Some wanted to embrace Judaism and traveled into the Pale of Settlement in order to learn more about Judaism. Upon learning this, the Russian government sent a number of priests to the Subbotniks to try to persuade them to return to Russian Orthodoxy. When the priests did not meet with any appreciable success, the government decided to suppress the Subbotniks with force. In 1826, the government decided to deport those who lived openly as Subbotniks to internal exile in the above-mentioned regions in the Caucasus, Transcaucasia, and Siberia. At the same time, it prohibited Jews and members of the Russian Orthodox Church from settling among any Subbotniks.
Subbotnik communities were among early supporters of Zionism. During the First Aliyah at the end of the 19th century, thousands of Subbotniks settled in Ottoman Palestine to escape religious persecution due to their differences with the Russian Orthodox Church. Their descendants include Israeli Jews such as Rafael Eitan and Alexander Zaïd. Major-General Alik Ron, former head of the Israeli Police's northern district, is also descended from some Subbotnik ancestors, as is the mother of Ariel Sharon.
The Subbotniks faced hurdles when intermarrying into the wider Jewish population, as they were not considered Jews according to halakha. They were noted for often being more religiously observant than the mostly secular Jewish Zionist population in that period. They Hebraized their surnames to assimilate. Within a short period, the descendants of Subbotnik Jews who arrived in Ottoman Palestine in the late 19th century had completely blended and inter-married into the wider Jewish population of Israel.
Subbotniks in Nazi-occupied areas of Ukraine were killed by Nazi soldiers and local Ukrainian collaborators due to their Jewish self-identity. They were relatively recent migrants to Ukraine from areas of Voronezh and considered outsiders by the peasants, who noted their practice of some Jewish customs. During the Holocaust, Nazis killed thousands of Subbotniks. By contrast, they did not attack Crimean Karaites, accepting the state's records that they were ethnic Russians (or Crimeans).
Following their massacre in the holocaust, the Subbotniks came to have an increasingly nationalist self-identification as Jews. However, after the War, the Soviet government ceased to recognize the "Subbotnik" as a legal ethnic category. They counted these people as a subset of the ethnic Russian population.
Between 1973-1991, the majority of Subbotniks of Ilyinki emigrated to Israel. After the fall of the Soviet Union, a few thousand Subbotniks left Russia for Israel. At this time, there was a mass emigration to Israel of more than a million ethnic Russian Jews and their immediate family members. Since that period, Subbotniks remaining in Russia have encountered status-related problems. The organization Shavei Israel, dedicated to reaching out to "lost Jews" and related communities, in the 21st century appointed a rabbi for the Subbotniks at Vysokaye, a town in Brest Oblast, Belarus. They intend to teach them Judaism, and encourage them to formally convert to Orthodox Judaism in order to be eligible for aliyah to Israel.
In the early 21st century there were complaints about certain members of the moshav Yitav, located in the Jordan Rift near Jericho in the territories. It was settled largely by Subbotniks from Georgia, Russia, in the 1970s; many had earlier created a commune in their town. In 2004 the Sephardic Chief Rabbi of Israel Shlomo Amar ruled the Subbotniks were not Jewish enough and would have to undergo an Orthodox conversion. The Interior Ministry classified the Subbotniks as a Christian sect and ineligible for aliyah to Israel, because no one knew if their ancestors had formally converted to Judaism (and there is much historic evidence that they did not). The ruling was under abolished in 2014, with an attempt by the Interior Ministry to allow remaining Subbotnik families to immigrate to Israel.
It has been difficult to estimate the exact number of Subbotniks in Russia at any given time. The discrepancies between government statistics and the membership have varied widely. Official data from czarist times placed the membership of the sect at several thousand. The writer E. Dinard, who was in personal contact with the Subbotniks, said in 1887 there were 2,500,000. Dinard may have included in his figures all of the Judaizing sects, and not just the Subbotniks, as this estimate is not supported by any other historians. Apart from their religious rites, the Subbotniks were generally indistinguishable from Russian Orthodox or secular Russians in terms of dress and lifestyle.