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Background  Mitochondrial DNA markers have long been used to identify population boundaries and are now a standard tool in conservation biology. In elasmobranchs, evolutionary rates of mitochondrial genes are low and variation between distinct populations can be hard to detect with commonly used control region sequencing or other single gene approaches. In this study we sequenced the whole mitogenome of 93 Critically Endangered Speartooth Shark  Glyphis glyphis  from the last three river drainages they inhabit in northern Australia.    Results  Genetic diversity was extremely low (π =0.00019) but sufficient to demonstrate the existence of barriers to gene flow among river drainages (AMOVA  Φ  ST  =0.28283,  P  <0.00001). Surprisingly, the comparison with single gene sub-datasets revealed that ND5 and 12S were the only ones carrying enough information to detect similar levels of genetic structure. The control region exhibited only one mutation, which was not sufficient to detect any structure among river drainages.    Conclusions  This study strongly supports the use of single river drainages as discrete management units for the conservation of  G. glyphis . Furthermore when genetic diversity is low, as is often the case in elasmobranchs, our results demonstrate a clear advantage of using the whole mitogenome to inform population structure compared to single gene approaches. More specifically, this study questions the extensive use of the control region as the preferential marker for elasmobranch population genetic studies and whole mitogenome sequencing will probably uncover a large amount of cryptic population structure in future studies.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-014-0232-x) contains supplementary material, which is available to authorized users.

Mitogenomics of the Speartooth Shark challenges ten years of control region sequencing