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Background  The cloacal tapeworm  Cloacotaenia megalops  (Hymenolepididae) is one of the most common cestode parasites of domestic and wild ducks worldwide. However, limited information is available regarding its epidemiology, biology, genetics and systematics. This study provides characterisation of the complete mitochondrial (mt) genome of  C. megalops .    Methods  The complete mt genome of  C. megalops  was obtained by long PCR, sequenced and annotated.    Results  The length of the entire mt genome of  C. megalops  is 13,887 bp; it contains 12 protein-coding, 2 ribosomal RNA and 22 transfer RNA genes, but lacks an  atp 8 gene. The mt gene arrangement of  C. megalops  is identical to that observed in  Anoplocephala magna  and  A. perfoliata  (Anoplocephalidae),  Dipylidium caninum  (Dipylidiidae) and  Hymenolepis diminuta  (Hymenolepididae), but differs from that reported in taeniids owing to the position shift between the tRNA (L1) and tRNA (S2) genes. The phylogenetic position of  C. megalops  was inferred using Maximum likelihood and Bayesian inference methods based on the concatenated amino acid data for 12 protein-coding genes. Phylogenetic trees showed that  C. megalops  is sister to  Anoplocephala  spp. (Anoplocephalidae) +  Pseudanoplocephala crawfordi  +  Hymenolepis  spp. (Hymenolepididae) indicating that the family Hymenolepididae is paraphyletic.    Conclusions  The complete mt genome of  C. megalops  is sequenced. Phylogenetic analyses provided an insight into the phylogenetic relationships among the families Anoplocephalidae, Hymenolepididae, Dipylidiidae and Taeniidae. This novel genomic information also provides the opportunity to develop useful genetic markers for studying the molecular epidemiology, biology, genetics and systematics of  C. megalops .    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-016-1782-0) contains supplementary material, which is available to authorized users.

Characterization of the complete mitochondrial genome of the cloacal tapeworm Cloacotaenia megalops (Cestoda: Hymenolepididae)