Havana, Cuba, is the birthplace of the mojito, although its exact origin is the subject of debate. It was known that the local South American Indians had remedies for various tropical illnesses, so a small boarding party went ashore on Cuba and came back with ingredients for an effective medicine. The ingredients were aguardiente de caña (translated as "burning water", a crude form of rum made from sugar cane) mixed with local tropical ingredients: lime, sugarcane juice, and mint. Lime juice on its own would have significantly prevented scurvy and dysentery, and tafia/rum was soon added as it became widely available to the British (ca. 1650). Mint, lime, and sugar were also helpful in hiding the harsh taste of this spirit. Another theory is that it was invented by Sir Francis Drake. The "El Draque" cocktail was prepared with brandy. While this drink was not called a mojito at this time, it was the original combination of these ingredients.

Some historians contend that African slaves who worked in the Cuban sugar cane fields during the 19th century were instrumental in the cocktail's origin. Guarapo, the sugar cane juice often used in mojitos, was a popular drink among the slaves who named it. It never originally contained lime juice.

There are several theories behind the origin of the name mojito: one such theory holds that name relates to mojo, a Cuban seasoning made from lime and used to flavour dishes. Another theory is that the name Mojito is simply a derivative of mojadito (Spanish for "a little wet"), the diminutive of mojado ("wet").

The mojito has routinely been presented as a favorite drink of author Ernest Hemingway. It has also often been said that Hemingway made the bar called La Bodeguita del Medio famous when he became one of its regulars and wrote "My mojito in La Bodeguita, My daiquiri in El Floridita" on a wall of the bar. This epigraph, handwritten and signed in his name, persists despite doubts expressed by Hemingway biographers about such patronage and the author's taste for mojitos. La Bodeguita del Medio is better known for its food than its drink.

A survey by an international market research company found that in 2016 the mojito was the most popular cocktail in Britain and France.

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