Abstract Eucoleus aerophilus (syn. Capillaria aerophila) is a trichuroid nematode affecting domestic and wild carnivores and, sometimes, humans. This parasite has a worldwide distribution and may cause significant clinical disease in pet animals. The present paper investigates the sequence variation in partial mitochondrial cytochrome c oxidase subunit 1 (cox1) gene of E. aerophilus isolates from pets and wild animals from different countries. Forty-four egg pools of E. aerophilus were collected from dogs, cats and foxes from Italy, while seventeen adult stages of E. aerophilus were obtained from red foxes and beech martens from Portugal, Romania, Serbia and UK. Fifteen different haplotypes were characterized and five were shared between pets in Italy and wildlife from Europe. The remaining haplotypes were either confined only in hosts or countries, or in a given host from a country. The phylogenetic analysis showed that all haplotypes clustered as a monophyletic group with a strong nodal support, indicating that all sequence types represented E. aerophilus. The results here presented have implications for a better understanding of the epidemiology, phylo-geography and clinical impact of E. aerophilus. In particular, the geographic distribution of E. aerophilus haplotypes in different host species and geographic regions, and their variation in terms of pathogenic impact and zoonotic role, warrant further investigations.