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Until the 19th century, the recording of baptisms, marriages and burials was largely the province of the church. When the Dutch East India Company (VOC) established its trading post at the Cape of Good Hope in 1652 it also established at that outpost the state church of the Netherlands, the Nederduits Gereformeerde Kerk (NGK) which remained, throughout the Company's rule an integral part of the Church in the Netherlands, subject to the ecclesiastical jurisdiction of the Amsterdam classis (governing body), its ministers being appointed by the Church authorities in the Netherlands and paid for by the VOC. 1
Until the appointment in 1665 of the first resident minister at the Cape, Johann van Arkel, baptisms were performed by visiting ministers on their way between the VOC's headquarters at Batavia (Indonesia) and the home country. Marriages could be performed by the Governor or by visiting ministers. Burials were naturally performed as and when necessary.
Some baptisms, marriages and deaths were recorded in the diaries kept by the Governors of the settlement, but the first permanent record was established by Ds. Van Arkel in 1665 from when baptisms and marriages were recorded in the register books of the Cape (later Cape Town) church. We have no burial or death registers from this period.
Until  the NGK was the only permitted church at the Cape, even though the mother country, the Netherlands, practiced a policy of practical toleration towards other religious sects. In that year a Lutheran church and congregation was permitted in Cape Town. Not until the British government assumed control of the Cape in 1805 were other Christian religions tolerated. The Muslim belief had been propagated and taken up from early days of the Dutch settlement, largely by slaves and freed slaves and their descendants, but what the attitude of the authorities toward this religion was is not known. The Muslim communities appear not to have kept registers of their members and the VOC did not recognise Muslim marriages. 2
In 1758 the Cape Government introduced the recording of deaths in the colony, a rather haphazard and perfunctory business at first, but by about 1800 the detail recorded was significant. These records survive in the Cape Archives3 and later, in 1834, were succeeded by the familiar, and still current, Death Notice system for recording deaths.4
By the time the British took over in 1805 there were around 8 Christian church congregations in the Cape recording baptism, births and, in some cases, burials. After that event the establishment of new congregation for many different sects and of missionary stations proliferated. I have not come across any comprehensive list of all the congregations established during the 19th century at the Cape and the records they kept.
Recently there has been a fair amount of work put in hand transcribing these registers and making these available in various formats, for instance Ockert Malan's magnificent transcription of the early Stellenbosch baptismal register5 published as a CD in 2004, and his very recent transcript of the Stellenbosch burial records6 and also a number of transcriptions commissioned by the web site Ancestry24.com, some available only to paying members and some available free of charge7. The web site e-family.co.za has also, for some time, housed a searchable database of transcripts done by Nolene Lossau from LDS Church microfilms, covering Cape, Orange Free State and Transvaal records.8
Also extremely useful in this context are the extracts transcribed by Sue Mackay from a number of Cape Newspapers housed in the National Archives, Kew. These transcripts are available on several web sites including the eGGSA Newspaper Library.
If I have omitted any other sources I will be happy to add them to this introduction.
1 Hattersley, Alan F. An illustrated social history of South Africa, A.A.Balkema, 1969, page 54
2 for further information see Shell, Robert - Children Of Bondage, a social history of the slave society at the Cape of Good Hope, 1652-1838, Witwatersrand University Press, 1994, page 356
3 Cape Archives, MOOC 6, Record of deaths at the Cape of Good Hope, 1758 - 1831
5 Stellenbosch Doopregister 1688-1732, Die
Genootskap vir die Kerkversameling, met vertolking deur
Ockert Malan & Lorna Newcomb.