Indigenous
mid 17th century: from Latin indigena ‘a native’ (see indigene) + -ous.
wiktionary
Borrowed from Late Latin indigenus(“native, born in a country”), from indi- ( indu-), an old derivative of in(“in”), gen- the root of gignō(“give birth to”), and English -ous. Compare indigene, Ancient Greek ἐνδογενής(endogenḗs, “born in the house”), and the separately formed endogenous.
etymonline
indigenous (adj.)
"born or originating in a particular place," 1640s, from Late Latin indigenus "born in a country, native," from Latin indigena "sprung from the land, native," as a noun, "a native," literally "in-born," or "born in (a place)," from Old Latin indu (prep.) "in, within" + gignere (perfective genui) "to beget, produce," from PIE root *gene- "give birth, beget," with derivatives referring to procreation and familial and tribal groups.
Indu "within" is from archaic endo, which is cognate with Greek endo- "in, within," from PIE *endo-, extended form of root *en "in." Related: Indigenously.