'nonindigenous' is an English formation combining the prefix 'non-' (from Latin 'non', meaning 'not') with 'indigenous'. 'Indigenous' ultimately originates from Latin 'indigena' and Greek 'indigēnos', where elements correspond to 'in-' ("in, within") and a root related to 'be born' (gign- / gen-).

'Indigenous' came into English via Latin 'indigena' (and Greek 'indigēnos') meaning 'native, born in a place'; it entered Middle English as 'indigenous' and developed into the modern adjective. The modern compound 'nonindigenous' is formed in English by adding the negating prefix 'non-' to that adjective to mean 'not indigenous.'

Originally 'indigenous' meant 'born in or produced in a particular place' (i.e., native). Over time that core meaning remained stable; 'nonindigenous' therefore developed as the straightforward negative sense 'not native; introduced from elsewhere.'