The present study investigates for the first time the presence of helminth eggs and worms in faeces from 107 wild and captive individuals collected from mid-March to mid-June 2010, and relates the findings to different environmental and host variables. Sixteen oxyurid species and the ascarid Angusticaecum holopterum were identified. This last nematode and the oxyurid species Tachygonetria palearticus and T. seurati had not been reported in Spanish wild T. graeca previously. The prevalence of oxyurid eggs and worms were 94%and 70%, respectively; while, ascarid eggs and worms were found in 26%and 5%of tortoises, respectively. Ascarid infections affected mostly captive animals and were associated to caparace deformities and symptoms of upper respiratory tract disease (p < 0.05). Oxyurid infections were not associated to negative health traits and prevalence increased with age. In free-living tortoises, the distribution of pharingodonid genera also varied according to habitat; moreover, T. longicollis, T. pusilla, T. conica, T. robusta and Mehdiella stylosa where significantly more frequent in wild compared to captive tortoises (p < 0.05). Study results highlight important differences in the nematode fauna of captive and free-living tortoises and questions one more time if the reintroductions of captive animals suppose a risk for the wild population since the former ones can harbor and distribute among free populations pathogens like ascarid nematodes.