The word ingenious sounds like the antonym (opposite) of genius as in- is often used as a negative suffix (invisible, indivisible, etc). However they are not.

Ingenious means:

– displaying genius or brilliance
– tending to invent
– characterized by genius
– cleverly done or contrived; witty; original; shrewd; adroit; keen; sagacious.

It comes from:

– the Middle French ingénieux (ingenious)

– from the Old French engenious (ingenious)

– from the Latin ingeniōsus ‎(endowed with good natural capacity, gifted with genius), from ingenium ‎(innate or natural quality, natural capacity, genius), from in ‎(in) and gignere ‎(to produce)

– from the Old Latin genere, from genus (birth, origin)

– from the Proto-Italic *genos (lineage, origin)

– from the Proto-Indo-European *ǵénh₁os ‎(race), from *ǵenh₁- ‎(to produce, beget).

Genius means:

– someone possessing extraordinary intelligence or skill; especially somebody who has demonstrated this by a creative or original work in science, music, art etc.
– extraordinary mental capacity
– inspiration, a mental leap, an extraordinary creative process
– the guardian spirit of a place or person (in Roman mythology)
– a way of thinking, optimizing one’s capacity for learning and understanding

It comes from:

– the Latin genius ‎(the guardian spirit of a person, spirit, inclination, wit, genius, literally “inborn nature”), from gignō ‎(to beget, produce)

– from the Old Latin genō

– from the Proto-Indo-European root *ǵenh₁- (see above)

So ingenious and genius come from the same root, as do many other words, but took different paths to arrive at their modern forms.

In Proto-Celtic the PIE root *ǵenh₁- became *gniyeti (to make, to do), which became gníid / ·gní (to do, to work) in Old Irish, which, with a suffix became dogní (to do, to make), which became déan in Modern Irish, jean in Manx and dèan in Scottish Gaelic. This is possibly also the root of the Welsh gwneud, the Cornish gul and the Breton (g)ober). All these words mean to do or to make.

Sources: Wiktionary