In this paper we outline the development of a spatial microsimulation model that uses a combinational optimisation technique called simulated annealing to match the Irish Census of Agriculture data to a National Farm Survey (NFS). The matched NFS and Census information is then used to produce small area farm population microdata estimates of the probability of participation by Irish farmers in the Rural Environmental Protection Scheme (REPS) for the year 2005. Previous studies that have examined the participation of farmers in agri-environmental schemes across Europe have been unable to quantify the type of habitats being protected under the programmes. This is rectified in this paper by combining the simulated farm population microdata with habitat land cover data within a GIS framework to examine what types of habitats are actually being protected under the agri-environmental programme. The results indicate that wetgrassland, bogland, rocky complexes, forestry and shallow water are habitats that are more likely to be given protection under the REPS programme while heath, dry grassland, built land and cut fen are habitat types that are unlikely to be protected under REPS. (C) 2008 Elsevier B.V. All rights reserved.