Botshabelo was established by the missionaries Alexander Merensky and Heinrich Grützner in 1865. Initially it provided a refuge for Black Christian fugitives, the need for this having arisen from the hostile conduct of the Bapedi chief Sekhukhune who forced the missionaries and their Bapedi converts to seek safety outside of Sekhukhune-land.

Merensky and Grützner were members of the Berlin Missionary Society, a large and influential body which established and ran numerous mission stations in the Transvaal and other parts of South Africa. The Transvaal was, however, its most prominent mission field.

In 1865 Merensky purchased the farm Boschhoek(now Toevlug) from Jan Abraham Joubert for 500 Prussian Thalers, and here Botshabelo was laid out. To protect themselves against attacks from Sekhukhune, the missionaries and their followers built a fort which was named Fort Wilhelm after the Prussian King Wilhelm I. This fort is now known as Fort Merensky and with its "Mediaeval" tower and walls that project above Botshabelo it is a unique  blend of Western and Sotho architecture.

The mission station which developed rapidly and in time became the most important, the largest and the best organised institution within the Berlin Missionary Society - a model mission indeed. It was self-suffient, with its cultivated fields, gardens, wainwright shop, brickyard, bakery, print-shop, mill and store. A German school was also established at the Mission and German Missionaries sent their children there.

Nevertheless the prime significance of Botshabelo lay in its function as a mission station. Shortly after Merensky's arrival, and as early as 1865, a small church (which still stands) was built. A parsonage and other buildings followed. Later on a much larger church, consecrated October of 1873, was erected. For many years this was the largest church  building in the Transvaal. This church - the masterpiece of Botshabelo - also stands to this day. A school for the children of baptised Blacks was established in 1873. A training school for catechists and evangelists followed in 1878. In 1906 a seminary for the training of teachers was created while a further primary school building was built in the 1930's and a high school with hostel in 1940.

A sanctuary indeed for many hundreds. By 1873 the Mission already housed 1 300 people, and in its prime as many as 3 000 lived here.

The halcyon days could not however continue indefinitely and in 1962, due to financial reasons, the Berlin  Missionary Society  began to withdraw from South Africa.

In April 1971, almost as an omen, the old church bell cracked during a church service. To the black people living  there it was a sign from above that their time at Botshabelo had ended. They left a year later to settle at Groblersdal among other places. After more than a hundred years of mission work a silence settled over the buildings, streets, lanes, gardens and fields of Botshabelo.