The protection of traditional knowledge by means of intellectual property rights is one of the major concerns of international organizations. Less attention has been paid to the relationship between systems of indigenous innovation and intellectual property. Using Australia as a case study, the paper argues that indigenous innovation systems are located within a connectionist cosmological framework. The distinctive institutional features of this innovation system are identified. Key is that innovation in systems maintains the health of other systems. The commodity-based nature of intellectual property systems does not suit this kind of innovation. Property rights in land matter to this innovation system far more than intellectual property. Forms of intellectual property based on the right to distinguish one’s product in the market will generally be more useful to indigenous innovation than commodity regimes such as the patent system. Voluntary certification systems can probably be harnessed to much greater effect by indigenous business enterprises.