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When he was born is unknown. 1875 is one of the dates previously mentioned, but this is clearly incorrect particularly if one considers the obituary written by D. E. Mbane that appeared in Imvo Zabantsundu following Sontonga's death on 18 April 1905. Mbane mentions that Sontonga was thirty-three years old when he died, which means that he must have been born in 1872. "He was not sick, except for a stomach ache. He was always saying he was going to die." On that account, he asked his wife one Sunday to take a photograph of him, but she had a toothache. As a result, he went to a professional photographer to have his portrait taken. His obituary mentions that he was a preacher and photographer. He was survived by his wife and a child.

Sontonga was born in Uitenhage and not at Lovedale Institution in Alice, as was previously believed. He was a member of the Mpinga clan (isiduko), which makes him Mpondomise, rather than Thembu as is sometimes claimed. Apparently, after being trained as a teacher at Lovedale, he was sent by the elders of the Methodist Church by ox wagon to Johannesburg, where he became an assistant teacher and choirmaster at the newly founded Methodist Church in Nancefield. According to his obituary, at the time of his death he was the choirmaster at the Rev. P. J. Mzimba Church in Johannesburg

Sontonga had a gift for song. He composed pieces, words and music for the use of his pupils at public entertainments. He wrote his compositions down in Tonic Sol-fa on odd sheets of paper, including Nkosi Sikelel' iAfrika, and eventually collected them into an exercise book with a view to publishing them. However, he died before he could achieve his ambition. He only wrote the first verse of Nkosi Sikelel' iAfrika. The Xhosa poet laureate, S. E. K. Mqhayi (1875-1945), wrote the additional seven verses of the hymn. Composed in 1897, Nkosi Sikelel' iAfrika was publicly sung in 1899 at the ordination of the Rev. M. Boweni, a Tsonga Methodist minister. The hymn was also commonly sung in Native Day Schools. The Ohlange Zulu Choir, which was founded by Rev. J. L. Dube, presented the hymn at concerts in Johannesburg and further popularised it.

Sontonga's portrait has an interesting history. In the early 1930's Professor D. D. T. Jabavu (1885-1959), of Fort Hare University, was approached by the editor of Lovedale Press, Mr Shepherd, for a portrait of E. M. Sontonga to be used in a forthcoming publication of sheet music devoted to Nkosi Sikelel' iAfrika and its history. In a letter dated 17 March 1934 Professor Jabavu informed Mr Shepherd that he had found a negative of a photograph of Sontonga taken by a Johannesburg photographer, S. Govo, who was a former Lovedale student, and he was forwarding a copy to Lovedale Press. When Lovedale Press burned down in the early 1960's the portrait of Sontonga and Jabavu's letter, which were fortunately at the editor's home, escaped being destroyed in the blaze and were subsequently donated to the museum. Sontonga was a keen photographer and on the day his portrait was taken he was walking round Johannesburg taking photographs with his camera. The bulge under his jacket, on the left of the portrait, apparently conceals his box camera.