Biodiversity resilience relies on genetic diversity, which sustains the persistence and evolutionary potential of organisms in dynamic ecosystems. Genomics is a powerful tool for estimating genome-wide genetic diversity, offering precise and accurate estimates of the status and trajectory of genetic diversity within species and populations. However, the widespread integration of genomic information into biodiversity conservation and management efforts faces challenges due to a lack of standardised genome-wide data generation methods and applications. The heterogeneity of approaches can make it difficult to consistently interpret the results and clearly communicate key information to stakeholders such as practitioners and decision-makers. To begin to address these challenges, the European Reference Genome Atlas (ERGA) promotes the standardisation of methodologies for high-quality reference genome sequencing and analysis as part of the global network of the Earth BioGenome Project. ERGA is also proactively developing best practices to engage stakeholders in biodiversity genomics research, starting with examining case studies and conducting mapping efforts to familiarise researchers with pathways to effective engagement. An emerging theme is the researchers’ experience of variable perceptions amongst stakeholders of the value and utility of reference genomes and genomics data in biodiversity conservation and management. Addressing this issue calls for consensus on standardised genome-wide data generation methods and applications that will help to deliver the highest standards for accuracy, interpretability, and comparability. We believe converging on consensus methods standardisation is essential for fostering the stakeholder trust and confidence required to successfully promote widespread adoption of genome-wide genetic diversity assessments in biodiversity conservation and management.