The authors performed whole-genome sequencing of almost the entire extant population of kākāpō (169 individuals). Reads were aligned to the kākāpō reference genome (bStrHab1.2.pri), and the DeepVariant analysis pipeline was used to call genetic variants. After filtering, a total of ~1.2 million high-quality SNPs and over 180,000 insertion–deletion mutations were identified across all sequenced birds. These variants were then used to determine inbreeding levels through subsequent generations of kākāpō, revealing that conservation efforts based on pedigree data have worked to reduce inbreeding and maintain genetic diversity. It is predicted that this high-quality variant dataset will further inform pedigree resources and assist in the prediction of genetic diversity in future individuals.