Elusor macrurus is an endangered short-necked turtle restricted to the Mary River catchment in south-eastern Queensland. Shotgun sequencing of genomic DNA was used to generate a complete mitochondrial genome sequence for E. macrurus using the Illumina MiSeq platform. The mitogenome is 16 499 base pairs (bp) long with 37 genes arranged in the typical vertebrate order and a relatively short 918-bp control region, which does not feature extensive tandem repeats as observed in some turtles. Primers were designed to amplify a 1270-bp region that includes 81% of the typically hypervariable control region. Two haplotypes were detected in a sample of 22 wild-caught individuals from eight sites across its natural range. The Mary River turtle is a species with low mtDNA nucleotide variability relative to other Chelidae. The combination of a very restricted distribution and dramatic reduction in population size due to exploitation for the pet trade are the conditions likely to have led to very low mtDNA variability in this endangered species.