In order to understand the meaning of the word "indigenous" , we have to break the word as
Indi + gen + ous
Here "Gen" means birth (like genesis: generation of something)
"Ous" means bearing some properties related to something
like marvelous : having property known as marvel.
Thus indigenous means having property of place where birth was taken
Thus it is originating in a particular region
The word root "gen" means "birth," and the suffix "-ous" means "having the quality of something."