The so-called ‘biotechnology clause’ of Article 27.3(b) of the WTO-TRIPS Agreement requires from member states protection for plant varieties either via the patent system or via an ‘effective sui generis system’ or by a combination of the two. Many developing countries prefer forms of sui generis protection, which allow them to include exceptions and protection measures for traditional agricultural practices and the traditional knowledge of farmers and local communities. However, ‘traditional knowledge’ remains a vaguely defined term. Its extension to biodiversity has brought a diffusion of the previously clearer link between protected subject matter, intellectual property and potential beneficiaries. The Philippine legislation attempts a ‘bottom-up’ approach focusing on the holistic perceptions of indigenous communities, whereas national economic interests thus far receive priority in India’s more centralist approach. Administrative decentralisation, recognition of customary rights, disclosure requirements, registers of landraces and geographical indications are discussed as additional measures, but their implementation is equally challenging. The article concludes that many of the concepts remain contested and that governments have to balance the new commercial incentives with the biodiversity considerations that led to their introduction, so that the system can be made sufficiently attractive for both knowledge holders and potential users of the knowledge.