It is a little bit odd to think of the notion of indigeneity being hegemonic since indigenous people have typically been oppressed rather than being in position to oppress others. However, it is possible in some instances for indigeneity to be hegemonic.
Indigeneity can be hegemonic when it is somehow beneficial to be indigeneous. This can happen in a few cases in which indigenous people have ended up with power. An example of this could be the case of Bolivia after the rise to power of Evo Morales, who identifies himself as indigenous. Another example could be that of Zimbabwe, where black Africans have identified themselves as indigenous and excluded whites from that definition. Finally, there is the example of some Native American nations in the US in which those who define indigeneity are in the position to determine who gets to benefit from the nations’ casino wealth.
In these cases, it may be possible for the dominant group (the indigenous people) to create a system in which other people see their exclusion and subordination as natural (the process of creating a hegemony). This can happen, for example, if those in the subordinate group feel that the dominant group has a superior claim to being indigenous. It is not necessarily the case that subordinate groups will buy into the hegemonic system, but it is at least possible.