Eucoleus aerophilus is the causative agent of respiratory capillariosis in wild and domestic carnivores and has sporadically affected humans. To date, this parasite has been detected in 38 countries, confirming its worldwide distribution. The aim of this study was to evaluate the prevalence of E. aerophilus in red fox populations from Central Europe and to describe the sequence variations in the partial cox1 gene of this parasite recovered from stool samples. An investigation was carried out using 342 samples of red foxes faeces investigated via seminested PCR and coproscopy. PCR results confirmed the presence of E. aerophilus DNA in 230 samples and E. boehmi DNA in 14 samples. Molecular analysis of the retrieved sequences revealed 22 haplotypes of E. aerophilus, EaPL1–EaPL22, and 4 haplotypes of E. boehmi, EbPL1–EbPL4. Coproscopic examination revealed that eggs of the Capillariidae family were most prevalent in all regions, with a mean prevalence of 73%. Furthermore, the following eggs were detected: Taeniidae (21.3%), Toxocara spp. (26.3%), Toxascaris leonina (5.3%), Trichuris vulpis (1.5%), trematodes (23.4%), hookworms (2.3%) and Mesocestoides spp. (1.8%). This study evaluated the prevalence of E. aerophilus in red fox populations in selected regions of Poland. To the best of our knowledge, this is the first molecular study on E. aerophilus in Poland.