Wedgefishes (Rhynchobatus spp) are significantly threatened by illegal trade globally due to their high-value fins on the international shark-fin market. There is an urgent need for better protection of wedgefish species including Rhynchobatus australiae, the bottlenose wedgefish and Rhynchobatus djiddensis, the whitespotted wedgefish. Few studies have investigated genetic variation in wedgefish populations, and there is a lack of molecular resources to further the knowledge needed to contribute to science-based development of fisheries and conservation management strategies for these species. The current study reports on the whole mitochondrial genomes of R. djiddensis and R. australiae, with the R. djiddensis mitogenome documented for the first time. We also aim to investigate the phylogenetic placement of R. djiddensis and R. australiae within the order Rhinopristiformes and to highlight the most variable gene regions to aid with primer design and the amplification of alternative mitochondrial markers. Future studies can utilize the genomic resources developed here to refine species identification and genetic characterization in these and related species.