late 13c., "overthrow, ruin," from Old French confusion (11c.) "disorder, confusion, shame," from Latin confusionem (nominative confusio) "a mingling, mixing, blending; confusion, disorder," noun of action from confundere "to pour together," also "to confuse" (see confound). Sense of "a putting to shame" (a sort of mental "overthrow") is late 14c. in English, while that of "mental perplexity" is from 1590s.
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