The mitochondrial genome of the Australia eastern long-necked turtle Chelodina longicollis is 16,437 bp, containing 37 genes, with overall gene organisation and nucleotide composition typical of mitogenomes of other vertebrates. We identified a presumptive light strand replication initiation site (OL) in the WANCY region, a feature thought to be absent from the side-necked turtles (Pleurodira). The tRNAser2 of C. longicollis lacks a D-arm. This is the fifth mitogenome published for the Pleurodira, the third for the Chelidae and the first turtle mitogenome generated using next-generation sequencing. It will assist the development of primers and strategies for examining mitochondrial variation across the side-necked turtles.