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Background  Infection with the parasitic nematode,  Baylisascaris schroederi  (Ascaridida: Nematoda), is one of the most important causes of death in giant pandas, and was responsible for half of deaths between 2001 and 2005. Mitochondrial (mt) DNA sequences of parasites can unveil their genetic diversity and depict their likely dynamic evolution and therefore may provide insights into parasite survival and responses to host changes, as well as parasite control.    Methods  Based on previous studies, the present study further annotated the genetic variability and structure of  B. schroederi  populations by combining two different mtDNA markers, ATPase subunit 6 ( atp6 ) and cytochrome c oxidase subunit I ( cox1 ). Both sequences were completely amplified and genetically analyzed among 57  B. schroederi  isolates, which were individually collected from ten geographical regions located in three important giant panda habitats in China (Minshan, Qionglai and Qinling mountain ranges).    Results  For the DNA dataset, we identified 20 haplotypes of  atp6 , 24 haplotypes of  cox1 , and 39 haplotypes of  atp6  +  cox1 . Further haplotype network and phylogenetic analyses demonstrated that  B. schroederi  populations were predominantly driven by three common haplotypes,  atp6  A1,  cox1  C10, and  atp6  +  cox1  H11. However, due to low rates of gene differentiation between the three populations, both the  atp6  and  cox1  genes appeared not to be significantly associated with geographical divisions. In addition, high gene flow was detected among the  B. schroederi  populations, consistent with previous studies, suggesting that this parasite may be essentially homogenous across endemic areas. Finally, neutrality tests and mismatch analysis indicated that  B. schroederi  had undergone earlier demographic expansion.    Conclusions  These results confirmed that  B. schroederi  populations do not follow a pattern of isolation by distance, further revealing the possible existence of physical connections before geographic separation. This study should also contribute to an improved understanding of the population genetics and evolutionary biology of  B. schroederi  and assist in the control of baylisascariasis in giant pandas.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-014-0606-3) contains supplementary material, which is available to authorized users.

Absence of genetic structure in Baylisascaris schroederi populations, a giant panda parasite, determined by mitochondrial sequencing