A fundamental problem in the identification of recovered Australian remains is that the current approach relies on forensic DNA methods developed for modern criminal casework, which are not suitable for degraded DNA. At the Griffith University’s Australian Research Centre for Human Evolution Ancient DNA Facility, we have been conducting pilot research involving DNA from the remains of a WWI Australian soldier recovered from Belgium. We have shown that advancements in extraction, next-generation sequencing and bioinformatics of ancient DNA provide a more informative approach for identifying fallen soldiers than traditional forensic methods alone. We successfully retrieved whole-genome data, revealed the maternal (mtDNA) and parental (Ych) haplotypes, and some phenotypic characteristics that can be used to target identification efforts. This pilot study highlights methodological advancements and the importance of genealogical searches of living relatives and their DNA to identify recovered remains and bring closure to their loved ones. Our methods have implications for future ancient DNA recovery efforts in facilities at the Queensland University of Technology and across Queensland.