The Brazilian cownose ray, Rhinoptera brasiliensis has undergone a global population reduction and is currently classified by IUCN as Vulnerable. We sequenced the complete mitochondrial genome of R. brasiliensis, resulting in a 17,759 bp genome size, featuring the typical vertebrate mitochondrial genome structure. The mtDNA genome contains 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a non-coding control region (D-loop). Each PCG was initiated by an authoritative ATG codon, except for COX1 that initiated by a GTG codon. Most of the PCGs were terminated by a complete codon (TAA/TAG), while an incomplete termination codon (TA/T) was found in five out of the 13 PCGs. Both Maximum Likelihood (ML) and Bayesian Inference (BI) analyses were used to reconstruct the phylogenetic relationships which revealed that R. brasiliensis was closely related to R. steindachneri whereas the reported mitogenome from a single specimen identified as R. steindachneri from Sri Lanka (GenBank accession number KM364982) was found to correspond to the sequence for R. javanica. These novel results provide a useful resource for further phylogeographic and population genetics studies of Rhinoptera spp.