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c.1300, "make uneasy, abash," from Anglo-French confoundre, Old French confondre (12c.) "crush, ruin, disgrace, throw into disorder," from Latin confundere "to confuse," literally "to pour together, mix, mingle," from com- "together" (see com-) + fundere "to pour" (see found (v.2)).
The figurative sense of "confuse, fail to distinguish, mix up" emerged in Latin, passed into French and thence into Middle English, where it is mostly found in Scripture; the sense of "destroy utterly" is recorded in English from c.1300. Meaning "perplex" is late 14c. The Latin past participle confusus, meanwhile, became confused (q.v.).