"certain, not doubtful," 1620s, from Latin indubius "not doubtful," from in- "not, opposite of" (see in- (1)) + dubius "vacillating, fluctuating," figuratively "wavering in opinion, doubting" (see dubious). Related: Indubiously.
word-forming element meaning "not, opposite of, without" (also im-, il-, ir- by assimilation of -n- with following consonant, a tendency which began in later Latin), from Latin in- "not," cognate with Greek an-, Old English un-, all from PIE root *ne- "not."
In Old French and Middle English often en-, but most of these forms have not survived in Modern English, and the few that do (enemy, for instance) no longer are felt as negative. The rule of thumb in English has been to use in- with obviously Latin elements, un- with native or nativized ones.
1540s, "puzzling, occasioning doubt or uncertainty;" 1630s, "doubtful, hesitating in opinion;" from Late Latin dubiosus "doubtful," from Latin dubium "doubt," neuter of dubius "vacillating, moving two ways, fluctuating;" figuratively "wavering in opinion, doubting, doubtful," from duo "two" (from PIE root *dwo- "two"), with a sense of "of two minds, undecided between two things." Old English also used tweo "two" to mean "doubt." Compare doubt (v.). Related: Dubiously; dubiousness.
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Harper, D. (n.d.). Etymology of indubious. Online Etymology Dictionary. Retrieved $(datetime), from https://www.etymonline.com/word/indubious