The koala (Phascolarctos cinereus), an iconic Australian marsupial, continues to experience severe population declines due to habitat loss, disease, and climate change, and is now listed as Endangered across eastern Australia. Effective conservation of koalas requires a standardised genomic tool to ensure data is directly comparable over time and space, strengthening conservation efforts. We therefore developed an integrated single nucleotide polymorphism (SNP) genotyping assay, incorporating ~5,000 informative loci derived from published genomic datasets, and novel SNPs identified from candidate fitness-related genes and major koala pathogen genomes/genes. This unified assay incorporates both host and pathogen markers, enabling comprehensive genomic monitoring through a single, streamlined workflow. The assay, which was validated using over 1,000 koalas collected across the species’ distribution, demonstrated high genotyping success and reproducibility across sample types including blood, tissue, urogenital swabs, hair, scat, and archived DNA. It supports multiple applications such as assessing population structure and connectivity, provenance, relatedness estimation, sex determination, and screening for pathogens including koala retrovirus and papillomavirus. The assay provides a robust, cost-effective framework for both fine- and broad-scale management by standardising data generation and comparison across studies and regions. By integrating host and pathogen genomics, this multi-purpose approach improves understanding of koala biology and strengthens evidence-based decision-making in conservation programs. The platform establishes a scalable model for wildlife genomics, enabling efficient, evidence-based management of threatened species.