Its widely supposed, as with many intoxicants used recreationaly, its simply a nickname coined by Mexican-Spanish speaking users who then introduced the word (and possibly the substance) into the US from where it spread elsewhere. Other places from where Cannabis Sativa had been introduced have had similar almost nonsensical words for it.
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Marijuana was a Mexican slang term for wild tobacco. It was then engraved into the culture with music and such, later adopted by the U.S government and the news paper companies to use for their nation wide campaign about its potential dangers.