This thesis develops a Decision Support System (DSS) to improve biosecurity response decisions affecting indigenous biodiversity. The key elements of the DSS are a synthesis of three components of non-market valuation: choice modelling, a systematic database of values and benefit transfer, with risk simulation to account for uncertainty. The innovative framework is demonstrated in a manual developed for Biosecurity New Zealand analysts for use during the early days of an incursion when time is severely constrained and uncertainty abounds. Theoretical approaches to decision making for environmental resource allocation decisions are reviewed with particular reference to decision support tools including non-market valuation, stated preference techniques, database development and benefit transfer. More complex and time consuming tools such as deliberative support and mediated modelling are also discussed. A framework is developed to quantify biodiversity values for use in Cost Benefit Analysis (CBA). The framework incorporates advanced choice modelling techniques demonstrated through four case studies, a systematic database of biodiversity values and transfer of these values using univariate benefit transfer with theoretical adjustment. The uncertainty in the values captured in the panel version of the Random Parameters Logit (RPL) model is integrated into CBA using risk simulation which utilises the means, standard deviations and correlation coefficients of risky variables to quantify the probability of achieving a positive Net Present Value of different response options. The DSS developed in this thesis has wider application in routine management of pests and diseases and in other resource allocation decisions by public agencies which impact on indigenous biodiversity.