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Triodontophorusspp. parasitizes the large intestine of equine, causing strongylid diseases. The present study assessed genetic variation in five gene regions within and betweenTriodontophorus brevicaudaandTriodontophorus nipponicusfrom Heilongjiang Province and the Inner Mongolia Autonomous region. The five gene markers were three mitochondrial (mt) genes, cytochromecoxidase subunit I (cox1), NADH dehydrogenase subunit 5 (nad5), cytochromeb(cytb); and two ribosomal RNA genes, the internal transcribed spacer 1 (ITS1) and the internal transcribed spacer 2 (ITS2). Partial (p) sequences ofcox1,nad5,cytb and the complete ITS rDNA region were PCR amplified from individual nematodes, and the amplicons were subjected to sequencing in both directions. The size of the three mt genes is identical in both species: 761 bp (pcox1), 505 bp (pnad5) and 562 bp (pcytb); the length of the two ribosomal genes is different: 376 bp and 370 bp (ITS1), and 333 bp and 322 bp (ITS2), respectively. Intraspecific variation betweenT. brevicaudaandT. nipponicuswas 0–1.5% and 0–1.1% for pcox1, 0–2.0% and 0–2.0% for pnad5, 0–1.4% and 0–2.2% for pcytb, 0–0.8% and 0–1.1% for ITS1 and 0–0.9% and 0–2.2% for ITS2. Interspecific variation within the nematodes was 13.5–14.3% for pcox1, 15.5–18.7% for pnad5, 16.7–18.6% for pcytb, 11.5–13.1% for ITS1 and 16.0–18.4% for ITS2. Phylogenetic analyses based on the combined mt gene sequences, as well as with the ITS sequences, show each species forming a monophyletic group of individuals. However, samples of different species from the same geographical origin did not always cluster together. These results provide valuable information for further studies of systematics and population genetics of the genusTriodontophorus. [ABSTRACT FROM PUBLISHER]