The involvement of Indigenous people in the national conservation effort is increasingly being acknowledged and valued in Australia. Ecological research can play an important role in reinforcing the efforts of Indigenous land managers; and interest from Indigenous and non-Indigenous ecologists and land managers to work together on ecological issues of common concern is increasing. Although there are many examples of successful collaborations there are also many instances where expectations, particularly of the Indigenous partners, are not met, and this is less frequently communicated. This paper, written from the perspective of an Arrernte researcher in partnership with his non-Indigenous colleague, outlines a range of challenges including the need for Indigenous people to have more control of what is done and why it is done on their country and to define and prioritise their own objectives for land management, which may or may not align with mainstream conservation agendas. Currently, Western conservation paradigms play the dominant role in how Natural Resource Management is practiced and how broader policy is set, and ecological research on Indigenous land is still most often led by the Western ecologists. This can leave out the ideas of Indigenous people and does little to address underlying inequitable power relationships. Indigenous Australians do not want to become spectators in the research process, giving away knowledge, or labourers to Western conservation agendas. They want to be active partners in developing better understandings of the environment and implementers of management that reflects shared agendas. Open discussion of these issues within the mainstream ecological literature is an important step towards change and will create better opportunities for both Indigenous and non-Indigenous ecological practitioners and Indigenous people dealing with land management policy.