Since the nineties of the last century two opposite trends have marked the development of international intellectual property protection. On the one hand, world trade negotiations have resulted in the establishment of a globally uniform system of adequate protection of intellectual property by the GATT/WTO Agreement on Trade Related Aspects of Intellectual Property Rights. It basically enshrines the market-oriented principles of protection of industrially developed countries. On the other, efforts to protect traditional and local knowledge have found specific support in the Convention on Biological Diversity which, in addition to providing, in the interest of environment protection, for mechanisms for the control of access to genetic resources, seeks to promote the condition of developing countries by subjecting such access to principles of prior informed consent and of participation in the benefit enterprises may obtain on the basis of patent protected inventions and innovations embodying or using genetic resources and associated traditional knowledge. The paper first examines the various ways in which biodiversity-related traditional knowledge may be passively or actively defended or protected, but concludes that, with the exception of a defence against misuses of the intellectual property system, little is to be expected from either reliance on existing forms of protecting intellectual property or from the development of more or less analogous forms of sui generis protection, the main reason being that intellectual property protection is a market-oriented mechanism, not a measure of knowledge conservation. In a second part the conflicts are analysed which arise when, as under the Biodiversity Convention, the market-oriented system of protection is put at the service of regulatory schemes aiming at non-market goals, in particular when the acquisition of patents is subject to additional and not directly related disclosure requirements, and when the exploitation of patents is conditioned on equitable benefit sharing. The main conclusion is that such burdening of patent protected innovation with specific environmental and developmental charges will result in negative synergies. These may have a counterproductive impact first, on the attainment of the regulatory objectives of protecting biodiversity and of promoting development and, second, on the technological neutrality of patent protection as an incentive mechanism for innovation in general. Additional problems of the legitimacy of using intellectual property as a support of objective-specific regulation suggest to implement the Convention on Biodiversity on the basis of a clearer separation between protection of biodiversity, promotion of development and stimulation of innovation, since this would bring it more in accordance with principles of proportionality regarding the selection and the use of regulatory instruments.