In 1859, Joseph Höttmann, a former associate of Wüst met with a group of Mennonites to discuss problems within the main Mennonite body. Their discussion centered on participating in communion with church members who were unholy or not converted and baptism of adults by immersion.
On January 6, 1860 this growing group of Mennonites influenced by a combination of Prussian Mennonite pietism, contacts with Moravian Brethren and indirectly through the influential preaching of Eduard Wüst, met in the village of Elisabeththal, Molotschna and formed the Mennonite Brethren Church. They felt the Mennonites had grown cold and formal, and were seeking greater emphasis on discipline, prayer and Bible study. The group presented a document to the elders of the Molotschna Mennonite Churches which indicated "that the total Mennonite brotherhood has decayed to the extent that we can no more be part of it" and fear the "approach of an unavoidable judgment of God. The immediate catalyst for the new organization was the discipline placed on a body of brethren who met to observe communion in a private home without the elders' sanction. The Mennonite Brethren were also in contact with and influenced by German Baptists J. G. Oncken and August Liebig.
The Mennonite Brethren movement spread throughout the Mennonite colonies and produced many distinguished leaders, particularly in Molotschna. These include P. M. Friesen (educator and historian), Jakob and Abraham Kroeker (writers), Heinrich Braun (publisher), Peter Braun (educator) and A. H. Unruh (educator). Jakob Kroeker (1872–1948) was one of the most prolific Mennonite writers, completing a fourteen volume Old Testament commentary. By breaking religious and cultural patterns that had become a hindrance to Mennonite society, the contribution of the Mennonite Brethren allowed all Mennonites groups in Russia to pursue a more wholesome Christian life.
Because of growing pressure by the Czarist government and later because of the political turmoil of the Russian Revolution significant number of the Mennonite Brethren moved to the United States, Canada, Paraguay and Mexico. In the Soviet Union their organizational structures ceased to exist by 1930 due to the Communist persecution. At that time some remaining Mennonite Brethren moved from Ukraine to the republics of the Soviet Central Asia. After World War II several Mennonite Brethren churches emerged in that region. In 1966 they joined the Evangelical-Baptist Union — an umbrella organization tightly controlled by the Soviet government.
Currently (2003), there are Mennonite Brethren congregations in more than 20 countries representing well over 300,000 believers. The largest conferences are the Conference of the Mennonite Brethren Church of India, with 103,488 members in 840 congregations, and the Communauté des Eglises de Frères Mennonites au Congo, with 85,648 members in 629 congregations. There are 225 congregations with 34,864 members in Canada, 188 congregations with 26,219 members in the United States, and 28 congregations with 1872 members in Japan. Some of the churches of the Bund Taufgesinnter Gemeinden in Germany are Mennonite Brethren (about 12 congregations). There are also 45 independent Mennonite Brethren congregations in Germany with 13,250 members.