The Dugong dugon (dugong) and Chelonia mydas (green sea turtle) are economically and culturally significant marine mega-herbivores whose populations are declining globally. Capture of these animals for study is challenging and stressful for the animals. Ecological questions can be answered using faeces, which can be collected floating on the water’s surface. However, green turtle and dugong faeces are visually indistinguishable. Specific PCR primer pairs were developed based on the mitochondrial control region of each species. We were able to determine species of origin using DNA extracted, amplified and sequenced from faeces. This provides a valuable tool for non-invasive taxonomic identification to assist the conservation of these vulnerable and endangered species.