The European wild rabbit (Oryctolagus cuniculus) is an introduced pest species in Australia and New Zealand. Rabbits have a devastating negative impact on agricultural production and biodiversity in these countries, and Rabbit Haemorrhagic Disease (RHD) is currently included in control strategies for rabbit populations. On the other hand, the European wild rabbit is a key native prey species in the Iberian Peninsula. Since the arrival of RHD, however, rabbit populations have undergone dramatic decreases and several predator species at risk of extinction are currently dependent on the rabbit population density. Therefore, from the point of view of biodiversity conservation, evaluating habitat correlates and trends of rabbit populations after the first RHD epizootic is of great interest to improve the long-term control or promotion of wild rabbit populations. We estimated the relationship between habitat factors and long-term population trends as well as the relationships between habitat factors and rabbit abundance 2 and 14 years after the arrival of RHD in several Iberian rabbit populations. We observed that only 26% of surveyed populations seemed to experience an increase in rabbit abundance over the last 12 years and that this increase was higher in the low-rabbit-abundance areas of l992, leading to high rabbit abundance in 2004. Our results suggested that short- and long-term impacts of RHD were related to habitat quality. The initial impact of RHD was higher in more suitable habitats, but increasing long-term population trends were positively related to good habitat quality.