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Background  Rumen flukes parasitize the rumen and reticulum of ruminants, causing paramphistomiasis. Over the years, there has been considerable debate as to whether  Paramphistomum leydeni  and  Paramphistomum cervi  are the same or distant species.    Methods  In the present study, the complete mitochondrial (mt) genome of  P. leydeni  was amplified using PCR-based sequencing and compared with that of  P. cervi . The second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA (rDNA) of  P. leydeni  specimens (n = 6) and  P. cervi  specimens (n = 8) was amplified and then sequenced. Phylogenetic relationship of the concatenated amino acid sequence data for 12 protein-coding genes of the two rumen flukes and selected members of Trematoda was evaluated using Bayesian inference (BI).    Results  The complete mt genome of  P. leydeni  was 14,050 bp in size. Significant nucleotide difference between the  P. leydeni  mt genome and that of  P. cervi  (14.7%) was observed. For genetic divergence in ITS-2, sequence difference between  P. leydeni  and  P. cervi  was 3.1%, while no sequence variation was detected within each of them. Phylogenetic analysis indicated that  P. leydeni  and  P. cervi  are closely-related but distinct rumen flukes.    Conclusions  Results of the present study support the proposal that  P. leydeni  and  P. cervi  represent two distinct valid species. The mt genome sequences of  P. leydeni  provide plentiful resources of mitochondrial markers, which can be combined with nuclear markers, for further comparative studies of the biology of  P. leydeni  and its congeners from China and other countries.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-015-0823-4) contains supplementary material, which is available to authorized users.

Mitochondrial and nuclear ribosomal DNA dataset supports that Paramphistomum leydeni (Trematoda: Digenea) is a distinct rumen fluke species