There is often considerable overlap between indigenous and autochthonic religions, but the two terms are used differently in the study of religions.
An indigenous religion is one where its symbolism and mythology largely relates to the culture of the people with whom it originated.
An autochthonic religion is one which 'sprang from the earth' - in other words it is based on a relationship with the land from which it came; it is not revealed from on high.
An example of an indigenous religion which is not autochthonic could be Judaism, because it is very much connected to being Jewish, but you can be Jewish anywhere, you don't have to be in Israel (though apparently it helps) and it is based on revelation from on high.
An example of an autochthonic religion which is not indigenous could be pantheism, because it is not revealed, but emerges from a relationship to the earth, but is not specific to a particular people. It's also not very organised, but there is a community of pantheists online, so it just about qualifies as a religion rather than just a belief.