While Johnson's identity is unknown, he demonstrates a knowledge of the sailor's speech and life, suggesting he could have been an actual sea captain. He could also have been a professional writer, well versed in the sea, using a pseudonym. If this is true, the name was perhaps chosen to reflect the playwright Charles Johnson, who had an unsuccessful play with The Successful Pyrate in 1712, which glamorized the career of Henry Avery and had been something of a scandal for seeming to praise a criminal. Following it, however, many authors would rush forward with biographies and catalogs of criminals, including catalogs of highwaymen and prostitutes. By this theory, the pseudonymous "Charles Johnson" of the pirate catalog was merely taking part in a burgeoning industry in criminal biography.

In 1934 John Robert Moore, an American scholar of Daniel Defoe, announced his theory that Johnson was really Daniel Defoe writing pseudonymously. He eventually published Defoe in the Pillory and Other Studies, in which he compared the style and contents of A General History to Defoe's works, noting that the frequent meditations on morality are similar to Defoe's work, and that Defoe wrote several other works on pirates. Moore's study, and his reputation as a Defoe scholar, was so convincing that most libraries recataloged A General History under Defoe's name. However, in 1988 scholars P. N. Furbank and W. R. Owen attacked the theory in The Canonisation of Daniel Defoe, in which they point out that there is no documentary evidence linking Johnson to Defoe, and that there are discrepancies between A General History and Defoe's other works.

The original publisher, Charles Rivington, emphasized the fact that the catalogue (largely assembled from newspaper accounts, Admiralty Court records and a few interviews) included stories of "the remarkable ACTIONS and ADVENTURES of the two Female Pyrates, Mary Read and Anne Bonny." A second edition, vastly enlarged and most likely assembled from writings by other authors than the original, came out within a few months. A German and Dutch translation were published in 1725. These German and Dutch language versions greatly played up the salaciousness of the accounts of "Amazon" pirates.

A General History of the Pyrates continues to be reprinted in many different editions, often with additional commentary, sometimes published under Charles Johnson's name and sometimes under Daniel Defoe's name. Nova Scotian author William Gilkerson published a 2006 children's novel Pirates Passage which was inspired by the life and work of Charles Johnson. (Reissued as The Brotherhood of Pirates. First published as 'Pirate's Passage' by Trumpeter Books, 2006.)

• Article comparing Defoe and Johnson
• Charles Johnson (1724), A General History of the Robberies and Murders of the Most Notorious Pyrates

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