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Background    Haemonchus contortus  is known among parasitic nematodes as one of the major veterinary pathogens of small ruminants and results in great economic losses worldwide. Human activities, such as the sympatric grazing of wild with domestic animals, may place susceptible wildlife hosts at risk of increased prevalence and infection intensity with this common small ruminant parasite. Studies on phylogenetic factors of  H. contortus  should assist in defining the amount of the impact of anthropogenic factors on the extent of sharing of agents such as this nematode between domestic animals and wildlife.    Methods    H. contortus  specimens ( n  = 57) were isolated from wild blue sheep ( Pseudois nayaur ) inhabiting Helan Mountains (HM), China and additional  H. contortus  specimens ( n  = 20) were isolated from domestic sheep that were grazed near the natural habitat of the blue sheep. Complete ITS2 (second internal transcribed spacer) sequences and partial sequences of the  nad 4 (nicotinamide dehydrogenase subunit 4 gene) gene were amplified to determine the sequence variations and population genetic diversities between these two populations. Also, 142  nad 4 haplotype sequences of  H. contortus  from seven other geographical regions of China were retrieved from database to further examine the  H. contortus  population structure.    Results  Sequence analysis revealed 10 genotypes (ITS2) and 73 haplotypes ( nad 4) among the 77 specimens, with nucleotide diversities of 0.007 and 0.021, respectively, similar to previous studies in other countries, such as Pakistan, Malaysia and Yemen. Phylogenetic analyses (BI, MP, NJ) of  nad 4 sequences showed that there were no noticeable boundaries among  H. contortus  populations from different geographical origin and population genetic analyses revealed that most of the variation (94.21%) occurred within  H. contortus  populations. All phylogenetic analyses indicated that there was little genetic differentiation but a high degree of gene flow among the  H. contortus  populations among wild blue sheep and domestic ruminants in China.    Conclusions  The current work is the first genetic characterization of  H. contortus  isolated from wild blue sheep in the Helan Mountains region. The results revealed a low genetic differentiation and high degree of gene flow between the  H. contortus  populations from sympatric wild blue sheep and domestic sheep, indicating regular cross-infection between the sympatrically reared ruminants.    Electronic supplementary material  The online version of this article (10.1186/s13071-017-2377-0) contains supplementary material, which is available to authorized users.

Genetic diversity of Haemonchus contortus isolated from sympatric wild blue sheep (Pseudois nayaur) and sheep in Helan Mountains, China