Major transitional challenges confront the former Soviet republics of Central Asia. These challenges include the withdrawal of subsidies from a centralized Soviet government, moves towards privatization and the conversion of administrative boundaries to international boundaries all within a short timeframe. The dissolution of the Soviet Union and emergence of independent States in its territory meant that many internal problems concerning the use, distribution and protection of natural resources have assumed a transboundary character.1 Transboundary strategies are therefore required to address the multiple resource use and protection issues in Central Asia. Globally, the practice of trans boundary watercourse management is significantly more developed than transboundary biodiversity conservation.2 Since 1948, 295 international water agreements have been recorded.3 In contrast there are few agreements aimed specifically at conserving biodiversity across an international boundary. The situation in Central Asia reflects global trends with the degree of attention given to the issue of transboundary water management eclipsing that of transboundary biodiversity conservation. While challenges remain for the transboundary management of Central Asian watercourses, the institutions, legal instruments and associated commentary and analysis are far more extensive than those for biodiversity conservation. This chapter will look to the experience of Central Asian transboundary water resource management to identify pitfalls and develop strategies for addressing the challenges to transboundary biodiversity conservation in the Pamir-Alai Land Management (PALM)4 transboundary project. The chapter first highlights the threats to the unique biodiversity in the PALM project area and the importance of trans boundary approaches and then sets out the complexities of transboundary water resource management in Central Asia. Existing regional agreements and institutions and the influence of Soviet era policies are explained as well as the main points of contention between upstream and downstream states. A summary of transboundary governance criteria and a comparison of the relative ease of fulfilling each criterion in the case of biodiversity conservation and freshwater management is provided. Following this, five criteria that have particular relevance in the comparison of transboundary water resource management in Central Asia and the PALM project are used to identify the areas for inter-sectoral learning in the management of Central Asian transboundary resources. The trans-sectoral comparison in the Central Asian context focuses on the importance of political buy-in; the equitable distribution of costs and benefits; effective legal and institutional frameworks; and dispute resolution mechanisms.