The problem of invasive alien species (IAS) is recognized as the second most serious threat to loss of biodiversity after habitat destruction. It is a problem largely created by humans as they transport and introduce species, deliberately and accidentally, from one part of the globe to another. The pressures exerted on biodiversity by international trade are one of the most serious aspects of the IAS problem. Although states are under obligations in international environmental law to prevent the entry of, and control, those alien species that threaten biodiversity, to date state practice has often been found wanting. In particular, quarantine regulation, which can be a state’s first line of defence against IAS, is mainly used by states to protect their farming and agricultural product sectors rather than biodiversity at large. The reasons for this include lack of domestic resources and lack of guidance at the international level. However, even if states were to expand the purview of quarantine, the question arises whether they would be able to use quarantine regulation to protect biodiversity from IAS while simultaneously fulfilling their international trade law obligations. This study seeks to answer this question by examining international environmental law and international trade law in their application to quarantine regulation. In doing so, the study identifies many areas of conflict. The different policies that underpin environmental and trade regimes mean that environmental concepts, such as the precautionary principle and the ecosystem approach, are difficult to apply within the international trade law regime. A way of achieving a more harmonized international response to the problem of IAS is suggested by incorporating environmental considerations into the international standards used by states to design and implement domestic quarantine measures. To facilitate the practical implementation of international standards the study further recommends appropriate financial and institutional capacity building mechanisms.