The European rabbit Oryctolagus cuniculus is a keystone species from the Iberian Peninsula where viral diseases have played a prominent role in regulating their populations. Coccidiosis, a parasitic disease caused primarily by Eimeria spp., is also thought to have important negative effects. However, few studies have investigated the impact of coccidia on wild European rabbit populations on the Iberian Peninsula. Here we estimate coccidian prevalence in rabbit faecal samples collected along transects established in two ecological regions. Six Eimeria species, with different pathogenicity, were identified (E. coecicola, E. perforans, E media, E. magna, E. irresidua and E. flavescens). Species diversity varied significantly between regions although mean oocyst excretion levels were generally low in both areas (57.61 s.d.±78.07 and 17.03 s.d.±27.72, oocyst per gram of rabbit faeces). This study is the first to describe the composition of the Eimeria spp. assemblage for wild rabbit populations on the Iberian Peninsula and provides fundamental information for future studies on the potential interaction of viral and parasitic diseases. ; Peer Reviewed