This paper explores the prospects and policy implications for bioenergy to contribute to a long-term sustainable UK energy system. The UK MARKAL technology-focused energy systems dynamic cost optimisation model which has been used to quantify the costs and benefits of alternative energy strategies in UK policy making is enhanced with detailed representation of bio-energy chains and end-uses. This provides an important advance in linking bioenergy expert-knowledge with a whole system modelling approach, in order to better understand the potential role of bioenergy in an evolving energy system. The new BIOSYS-MARKAL model is used to run four scenarios constructed along the pillars of UK energy policy objectives (low carbon and energy security). The results are analysed in terms of bioenergy resources use and bioenergy pathways penetration in different end use sectors. The main findings suggest that the complexity of different bioenergy pathways may have been overlooked in previous modelling exercises. A range of bioenergy pathways notably bio-heat and biofuels for transport may have a much wider potential role to play. The extent to which this potential is fulfilled will be further determined by resources availability, and market segment constraints, as well as policy measures to improve deployment. (C) 2010 Elsevier Ltd. All rights reserved.