Background. There is an extensive area of introgressive hybridization of the sable and the pine marten in Western Siberia. MtDNA haplotypes mark different phyletic lines of mustelids and can be used to identify their hybrids. Natural focus of filaroidosis, nematodes pathogenic to martens, is situated in Western Siberia. We hypothesized that groups of mustelids different in origin have different susceptibility to nematode infestation. Materials and methods. Animals were caught according to the hunting license in 2009-2014, in 9 localities of Western Siberia. A total of 166 individuals, including 100 sables, 20 pine martens and 46 their hybrids (kidus) were investigated using the method of dissection of the gastrointestinal tract and lungs. Polymorphism of the mitochondrial cytochrome b gene was studied by the method of RFLP (Restriction Fragment Length Polymorphism). Results. Four species of parasitic nematodes Crenosoma petrovi, Filaroides martis, Capillaria putorii, Strongyloides martis were found in martens in Western Siberia. The pine marten was infected by F. martes and S. martis more than the sable (p ˂ 0.05). Hybrids had intermediate levels of nematode infestation. 9 complex haplotypes of mtDNA were identified. Haplotype Z30 prevailed in the sable, AK29 and Z5 - in the pine marten, Z30 and AK23 - in hybrids. Animals from different lines of mtDNA differed significantly by helminths infestation. Animals with a haplotype Z31, typical of the eastern subspecies of sable, were infected with helminths in 2 times more than the animals from Z5 and Z30 lines, typical of the local populations. Animals with a haplotype AK23 have the lowest rate of infections by helminths. Conclusion. Differences in nematode infestation of animals with different mtDNA haplotypes indicates that different phyletic lines of the sable, the pine marten, and their hybrids have varying degrees of susceptibility to nematode infestations.