Despite increased conservation efforts, the European rabbit (Oryctolagus cuniculus), a keystone species in the Iberian Peninsula, continues declining due to habitat degradation and viral diseases. Following the 2011 outbreak of Rabbit Hemorrhagic Disease virus GI.2, the species was listed as Endangered by the International Union for Conservation of Nature (IUCN). While rabbit declines in natural habitats are well documented, no research has separately analyzed population trends between areas where rabbits are managed as agricultural pests (rabbit emergency hunting areas: REHAs) and other areas, mostly natural (non-REHAs). Additionally, recent findings suggest divergent trends between the two rabbit subspecies, O. c. cuniculus and O. c. algirus, which coexist only in a limited area where their ranges overlap, with the latter possibly experiencing a more widespread decline. Here, we analyzed hunting yield data from ~ 6,000 hunting estates in Castilla-La Mancha (central Spain), spanning 2009 to 2022. Using linear mixed models (GLMMs), we found significant differences in rabbit hunting yields and trends between REHAs and non-REHAs, as well as between the subspecies’ distribution areas. Densities of hunted rabbits were higher in REHAs, while the lowest hunting yields were observed in O. c. algirus areas, consistent with studies suggesting its lower abundance. Population trends in non-REHAs showed declines for both subspecies, with a less pronounced decrease in O. c. cuniculus areas and near stability in REHAs inhabited by this subspecies. These findings reveal contrasting trends between subspecies and management areas, emphasizing the need for targeted management strategies tailored to agricultural and natural habitats and the specific ecological requirements of each subspecies.