Etymology
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miso- 

word-forming element of Greek origin meaning "hater, hatred," before vowels, mis-, from Greek misos "hatred," misein "to hate," of uncertain etymology, perhaps from a Pre-Greek word. It was productive as a word-forming element in ancient Greek, for instance misoagathia "hatred of good or goodness;" misoponein "to hate work." In English it formed many compounds now obscure or recherche, but some perhaps still useful, such as  misocapnic (adj.) "hating (tobacco) smoke," misocyny "hatred of dogs," misoneism "hatred of novelty."

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in- (1)
Origin and meaning of in-
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.
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