Madagascar occupied the attention of the Directors of the Missionary Society from its inception, and a Mission was proposed as early as 1797. In 1814 John Le Brun arrived in Mauritius, and as a consequence Port Louis then served as a base to launch mission activity in Madagascar. In 1818, two Welsh missionaries David Jones and Thomas Bevan started a mission at Tamatave. In less than 3 months, only Jones remained alive from the two families. After this false start, a mission was founded at Antananarivo in 1820, with the support of Chief Radama. The mission was reinforced by David Griffiths and John Jeffreys, and the task of translating the Bible into Malagasy was started. David Johns arrived in Madagascar 1826.
Queen Ranavalona succeeded the throne after Radama's death, and despite initial reassurances that Indigenous people could be baptised, there was anti-missionary feeling and local Christians were killed. On 26 Feb 1835 the Queen issued a decree that the missionaries could not convert local people. This sparked a period of religious repression and the LMS missionaries left the Island by July 1836. Many local converts were killed, although many buried religious texts to attempt to preserve them. The repression lasted until 1861 when the new King Radama II allowed religious liberty and missionaries returned. The period of greatest advance came after Queen Ranavalona II's accession in 1868, as she converted to Christianity. The LMS worked on training Indigenous pastors and providing education facilities and the number of churches and missions grew.
In 1896 Madagascar became a French colony and there was suspicion that LMS missionaries were involved in anti-government activities. Despite these problems the Madagascar mission flourished, due in part to missionaries such as Elizabeth Lomas, James Sibree and Percy Milledge. Despite reduction in the number of LMS missionaries, they were able to continue their work. Progess was made towards a self-supporting Church. Later missionaries included James Hardyman.
The post-war period was marked by devolution and moves towards church union. In 1961 the LMS churches became the Church of Christ in Madagascar.