General Antonyms:
* Foreign
* Non-native
* Exotic
* Alien
* Introduced
* Imported
* Extraneous
Antonyms Related to Origin:
* Introduced
* Naturalized
* Colonized
* Immigrant
Antonyms Related to Culture:
* Assimilated
* Acculturated
* Westernized
* Modernized
Specific Examples:
* Indigenous plant: Introduced plant
* Indigenous people: Immigrants
* Indigenous language: Foreign language
The best antonym for "indigenous" will depend on the specific context and the meaning you want to convey.