It’s pretty arbitrary. In the broader sense, the word refers to any native flora or fauna that evolved in that location, and so its use in the human context doesn’t make much sense. Basically, people use the term to mean any group of people who were living in a place before Europeans or other imperialists arrived. People commonly accept that humans did not originate in the Americas, but still the people whose ancestors were there before white people are called “indigenous” even though their ancestors also came from somewhere else. In Japan, it’s the Ainu who were there before the next group of people from the mainland arrived. And so on.