The City of Aberdeen had only one Parish Church (St Nicholas) from 1060 until the year 1828 when the Court of Teinds decided that there should be six Parishes. These were East and West St Nicholas, St Clement's and Greyfriar's (each based on existing churches) and The North and South Parishes for which new churches would be built.

At the disruption in 1843 the East, West and South congregations built three places of worship together, at the corner of Belmont Street and Schoolhill. In 1892 the congregation of the South Parish moved into the present building, designed by A Marshall Mackenzie and featuring a giant portico surmounted by a drum and high dome, modelled on St Paul's Cathedral.

In 1972 as the result of the retiral of the then minister, Rev. Doctor James Wood MA DD the South Church united with the East and Belmont Church and the new congregation took the name, St Mark's. As a result of the discovery of dry rot in their buildings at Crown Street the congregation of Trinity Church (who had been worshipping in St Mark's for some time following a fire) united with St Mark's in 1981.

Between 1986 and 1989 there was a protracted vacancy which was caused by the uncertainty of the congregation's right to call a minister. However after long discussion and two major debates in Presbytery the congregation won the right to an unrestricted call which resulted in the arrival of the present minister, Rev John Mutch Watson.