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The presence of Orthodox Christianity in Botswana is a recent event. Orthodox Christianity missionary efforts in Botswana began in the late twentieth century under the jurisdiction of the Church of Alexandria. Currently, Botswana is within the local jurisdiction of a new diocese, the Holy Diocese of Botswana.

The Diocese of Botswana was a part of the Archdiocese of Zimbabwe until it was detached on October 7, 2010 and placed under the leadership of His Grace Bishop Gennadios of Nilopolis. Bp. Gennadios was enthroned as the first Bishop of Botswana on June 2, 2012 by Pope Theodoros II of Alexandria in the Anglican Cathedral of the Holy Cross in Gaborone, Botswana.

Communities of the diocese include the Church of St. Nicholas (including the chapels of St. Parthenios Bishop of Lampsakos and St. Peter Archbishop of Alexandria) in Gaborone.