<p>Avian haemosporidia are vector-borne protozoan parasites with effects ranging from asymptomatic infections to acute disease and are often influenced by host‒parasite dynamics and environmental factors. These parasites can disrupt haematological parameters, affecting host fitness and survival. The African houbara (<i>Chlamydotis undulata</i>), a vulnerable species supported by a conservation breeding program in Morocco, faces combined threats from habitat loss, unregulated hunting, and poaching. This study investigated the diversity, prevalence and potential factors of haemosporidian infections in captive African houbara and assessed the association between infection and changes in blood parameters. To assess haemosporidian prevalence across sex and age groups, we analysed tissue samples (liver and spleen) collected during necropsy from 264 individuals from two breeding centres and two release facilities. Additionally, we used thin blood smears and cell pellets from 64 apparently healthy adults to evaluate haematological changes. Molecular (PCR-based detection and sequencing) and blood smear screening identified infections by <i>Haemoproteus</i> (85.9%) and <i>Plasmodium</i> (14.1%), revealing five previously undetected lineages. Coinfections were documented, highlighting challenges in diagnostic accuracy and parasite interactions. Age, location and sampling year significantly influenced infection prevalence, but no impact of infection on blood parameters was detected, consistent with a subclinical state. The high prevalence observed, along with the detection of previously undescribed lineages, underscores the importance of continued research on haemosporidian species and their potential impact on avian species, particularly in the context of conservation programmes.</p> Graphical Abstract <p></p>