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Background    Fasciolopsis buski  is a zoonotic intestinal fluke infecting humans and pigs, but it has been seriously neglected. It is yet to know whether there is any genetic diversity among  F. buski  from different geographical locations, particularly in sequences of nuclear ribosomal DNA (rDNA) and mitochondrial (mt) DNA. Therefore, we determined the sequences of partial 18S, the complete internal transcribed spacer (ITS) rDNA and the complete mt genome of  F. buski  from China, compared the rDNA and mtDNA sequences with those of isolates from India and Vietnam, and assessed the phylogenetic relationships of this fluke and related fasciolid trematodes based on the mtDNA dataset.    Results  The complete mt genome sequence of  F. buski  from China is 14,833 bp, with 36 genes, including 12 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes ( rrn L and  rrn S). The AT content of  F. buski  from China is 65.12%. The gene content and arrangement of the  F. buski  mt genome is similar to that of  Fascioloides magna . Genetic distances between isolates of  F. buski  from China and India were high (28.2% in mtDNA, 13.2% in ITS-1 and 9.8% in ITS-2) and distinctly higher than the interspecific differences between  Fasciola hepatica  and  Fasciola gigantica . The rDNA and mtDNA datasets for  F. buski  from China (isolate from pigs) and Vietnam (isolates from humans) were identical. The intergeneric differences in amino acid and nucleotide sequences among the genera  Fasciolopsis ,  Fascioloides  and  Fasciola  ranged between 24.64–25.56% and 26.35–28.46%, respectively.    Conclusions  Our results indicate that  F. buski  from China and India may represent distinct taxa, while  F. buski  in Vietnam and China represent the same species. These findings might have implications for the implementation of appropriate control strategies in different regions. Further studies are needed to decode mtDNA and rDNA sequences of  F. buski  from various geographical isolates for the better understanding of the species complex of  F. buski .    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-017-2039-2) contains supplementary material, which is available to authorized users.

Fasciolopsis buski (Digenea: Fasciolidae) from China and India may represent distinct taxa based on mitochondrial and nuclear ribosomal DNA sequences