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<p>Abstract</p> <p>Background</p> <p>Studying mitochondrial (mt) genomics has important implications for various fundamental areas, including mt biochemistry, physiology and molecular biology. In addition, mt genome sequences have provided useful markers for investigating population genetic structures, systematics and phylogenetics of organisms. <it>Toxocara canis, Toxocara cati </it>and <it>Toxocara malaysiensis </it>cause significant health problems in animals and humans. Although they are of importance in human and animal health, no information on the mt genomes for any of <it>Toxocara </it>species is available.</p> <p>Results</p> <p>The sizes of the entire mt genome are 14,322 bp for <it>T. canis</it>, 14029 bp for <it>T. cati </it>and 14266 bp for <it>T. malaysiensis</it>, respectively. These circular genomes are amongst the largest reported to date for all secernentean nematodes. Their relatively large sizes relate mainly to an increased length in the AT-rich region. The mt genomes of the three <it>Toxocara </it>species all encode 12 proteins, two ribosomal RNAs and 22 transfer RNA genes, but lack the ATP synthetase subunit 8 gene, which is consistent with all other species of Nematode studied to date, with the exception of <it>Trichinella spiralis</it>. All genes are transcribed in the same direction and have a nucleotide composition high in A and T, but low in G and C. The contents of A+T of the complete genomes are 68.57% for <it>T. canis</it>, 69.95% for <it>T. cati </it>and 68.86% for <it>T. malaysiensis</it>, among which the A+T for <it>T. canis </it>is the lowest among all nematodes studied to date. The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. The mt genome structures for three <it>Toxocara </it>species, including genes and non-coding regions, are in the same order as for <it>Ascaris suum </it>and <it>Anisakis simplex</it>, but differ from <it>Ancylostoma duodenale</it>, <it>Necator americanus </it>and <it>Caenorhabditis elegans </it>only in the location of the AT-rich region, whereas there are substantial differences when compared with <it>Onchocerca volvulus</it>,<it>Dirofiliria immitis </it>and <it>Strongyloides stercoralis</it>. Phylogenetic analyses based on concatenated amino acid sequences of 12 protein-coding genes revealed that the newly described species <it>T. malaysiensis </it>was more closely related to <it>T. cati </it>than to <it>T. canis</it>, consistent with results of a previous study using sequences of nuclear internal transcribed spacers as genetic markers.</p> <p>Conclusion</p> <p>The present study determined the complete mt genome sequences for three roundworms of human and animal health significance, which provides mtDNA evidence for the validity of <it>T. malaysiensis </it>and also provides a foundation for studying the systematics, population genetics and ecology of these and other nematodes of socio-economic importance.</p>