INTRODUCTION: The blue peafowl (Pavo cristatus) and the green peafowl (Pavo muticus) have garnered significant public affection due to their stunning appearance, although the green peafowl is currently endangered. The causative mutation that causes the leucistic plumage of the blue peafowl (also called white peafowl) remains unknown. RESULTS: In this study, we generated a chromosome-level reference genome of the blue peafowl with a contig N50 of 30.6 Mb, including the autosomes, Z and W sex chromosomes, and a complete mitochondria DNA sequence. Data from 77 peafowl whole genomes, 76 peafowl mitochondrial genomes, and 33 peafowl W chromosomes genomes provided the first substantial genetic evidence for recent hybridization between green peafowls and blue peafowls. We found 3 hybrid green peafowls in zoo samples rather than in the wild samples, with a blue peafowl genomic content of 16-34%. Maternal genetic analysis showed that 2 of the hybrid female green peafowls contained complete blue peafowl mitochondrial genomes and W chromosomes. Some animal protection agencies release captive green peafowls in order to maintain the wild population of green peafowls. Therefore, to better protect the endangered green peafowl, we suggest that purebred identification must be carried out before releasing green peafowls from zoos into the wild in order to prevent the hybrid green peafowl from contaminating the wild green peafowl. In addition, we also found that there were historical introgression events of green peafowl to blue peafowl in 4 zoo blue peafowl individuals. The introgressed genomic regions contain IGFBP1 and IGFBP3 genes that could affect blue peafowl body size. Finally, we identified that the nonsense mutation (g.4:12583552G>A) in the EDNRB2 gene is the genetic causative mutation for leucistic plumage of blue peafowl, preventing melanocytes from being transported into plumage, thereby inhibiting melanin deposition. CONCLUSION: Our research provides both theoretical and empirical support for the conservation of the endangered green peafowl. The high-quality genome and genomic data also provide a valuable resource for blue peafowl genomics-assisted breeding.