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Although the song's origin is uncertain, its subject may be Charles Edward Stuart ('Bonnie Prince Charlie') after the defeat of the Prince at the Battle of Culloden in 1746 and his subsequent exile, his Jacobite supporters could have sung the tune in his honour; and thanks to the ambiguity of the term "bonnie", which can refer to a woman as well as to a man, they could pretend it was a love song.
In 1881, under the duo of pseudonyms H.J. Fuller and J.T. Wood, Charles E. Pratt published sheet music for "Bring Back My Bonnie to Me". Theodore Raph in his 1964 book American song treasury: 100 favorites, writes that people were requesting the song at sheet music stores in the 1870s, and Pratt was convinced to publish a version of it under the pseudonyms, and the song became a big hit, especially popular with college singing groups but also popular for all group singing situations