in- (1) Look up in- at Dictionary.com
prefix meaning "not, opposite of, without" (also im-, il-, ir- by assimilation of -n- with following consonant), from Latin in- "not," cognate with Greek an-, Old English un-, from PIE *ne "not" (see un- (1)).
in- (2) Look up in- at Dictionary.com
element meaning "into, in, on, upon" (also im-, il-, ir- by assimilation of -n- with following consonant), from Latin in- "in" (see in). In Old French this often became en-, which usually was respelled in English to conform with Latin, but not always, which accounts for pairs like enquire/inquire. There was a native form, which in West Saxon usually appeared as on- (as in Old English onliehtan "to enlighten"), and some verbs survived into Middle English (such as inwrite "to inscribe"), but all now seem to be extinct. Not related to in- (1) "not," which also was a common prefix in Latin: to the Romans impressus could mean "pressed" or "unpressed."