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Background  Representatives of the trematode family Fasciolidae are responsible for major socio-economic losses worldwide.  Fascioloides magna  is an important pathogenic liver fluke of wild and domestic ungulates. To date, only a limited number of studies concerning the molecular biology of  F. magna  exist. Therefore, the objective of the present study was to determine the complete mitochondrial (mt) genome sequence of  F. magna , and assess the phylogenetic relationships of this fluke with other trematodes based on the mtDNA dataset.    Findings  The complete  F. magna  mt genome sequence is 14,047 bp. The gene content and arrangement of the  F. magna  mt genome is similar to those of  Fasciola  spp . , except that  trn E is located between  trn G and the only non-coding region in  F. magna  mt genome. Phylogenetic relationships of  F. magna  with selected trematodes using Bayesian inference (BI) was reconstructed based on the concatenated amino acid sequences for 12 protein-coding genes, which confirmed that the genus  Fascioloides  is closely related to the genus  Fasciola ; the intergeneric differences of amino acid composition between the genera  Fascioloides  and  Fasciola  ranged 17.97–18.24 %.    Conclusions  The determination of  F. magna  mt genome sequence provides a valuable resource for further investigations of the phylogeny of the family Fasciolidae and other trematodes, and represents a useful platform for designing appropriate molecular markers.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-016-1699-7) contains supplementary material, which is available to authorized users.

Complete mitochondrial genome of the giant liver fluke Fascioloides magna (Digenea: Fasciolidae) and its comparison with selected trematodes