In the past two decades, the relationship between the Convention on Biological Diversity and multilateral trade obligations administered by the World Trade Organization has no doubt been one of the most well-known case studies within the ‘trade-and-environment’ debate. Commentators have especially focused on the potential conflict with the WTO agreements arising from restrictions on trade in genetically modified organisms as well as from the CBD provisions on access to genetic resources and sharing of benefits resulting from their utilization. Following the Nagoya Protocol, both issues are now regulated under protocols to the CBD. As the purpose of these protocols is to operationalize the programmatic and frequently vague provisions of the CBD, it is foreseeable that, as already occurred with the Cartagena Protocol, the adoption and implementation of the Nagoya Protocol will generate a new wave of enhanced policy and scholarly discussions on its compatibility with the world trade system. After a preliminary consideration of the scope of the NP and the nature of its obligations, this chapter will present an overview of the main substantive trade issues arising from the Protocol. Essentially, these concern the relationship between the Protocol’s ABS regime and WTO agreements on trade in goods and that between the Protocol and WTO obligations in the field of intellectual property rights. The next part of the chapter will revisit the systemic issue of the relationship between trade rules and the biodiversity regime in the light of the specific clause of Article 4 of the Nagoya Protocol and of pertinent WTO negotiations. I conclude with a summary of the reasons why the Nagoya Protocol fails to meet the expectation of an agreement laying down clear rules in the trade-and-biodiversity area.