1530s, "to have doubts (of the reality of), to suspect, to regard (the truth or reality of) with suspicion," from mis- (1) "badly, wrongly" + doubt (v.). Meaning "to fear or suspect (the existence of something evil) is from 1560s. Intransitive sense of "entertain doubt" is from 1630s. Related: Misdoubted; misdoubting. As a noun, "irresolution," 1590s.
prefix of Germanic origin affixed to nouns and verbs and meaning "bad, wrong," from Old English mis-, from Proto-Germanic *missa- "divergent, astray" (source also of Old Frisian and Old Saxon mis-, Middle Dutch misse-, Old High German missa-, German miß-, Old Norse mis-, Gothic missa-), perhaps literally "in a changed manner," and with a root sense of "difference, change" (compare Gothic misso "mutually"), and thus possibly from PIE *mit-to-, from root *mei- (1) "to change."
Productive as word-forming element in Old English (as in mislæran "to give bad advice, teach amiss"). In 14c.-16c. in a few verbs its sense began to be felt as "unfavorably," and it came to be used as an intensive prefix with words already expressing negative feeling (as in misdoubt). Practically a separate word in Old and early Middle English (and often written as such). Old English also had an adjective (mislic "diverse, unlike, various") and an adverb (mislice "in various directions, wrongly, astray") derived from it, corresponding to German misslich (adj.). It has become confused with mis- (2).