Giraffes, which consist of four major lineages—Northern, Reticulated, Masai, and Southern—show strong genetic divergence despite being geographically close. A comprehensive analysis of whole-genome sequencing data from 90 wild giraffes across their range reveals a complex evolutionary history marked by significant gene flow, particularly affecting the Reticulated lineage. The Reticulated lineage is identified as a hybrid lineage, with contributions from both the Northern and an ancestral lineage related to Masai and Southern giraffes. This study highlights the importance of considering diversity within giraffes for effective conservation, including reintroductions and population management strategies. The findings also suggest that reproductive barriers between major giraffe lineages may have evolved more recently, as captive and wild hybrids have been documented. The study provides genomic resources that are crucial for maintaining genetic diversity across major lineages and sublineages of giraffes.Giraffes, which consist of four major lineages—Northern, Reticulated, Masai, and Southern—show strong genetic divergence despite being geographically close. A comprehensive analysis of whole-genome sequencing data from 90 wild giraffes across their range reveals a complex evolutionary history marked by significant gene flow, particularly affecting the Reticulated lineage. The Reticulated lineage is identified as a hybrid lineage, with contributions from both the Northern and an ancestral lineage related to Masai and Southern giraffes. This study highlights the importance of considering diversity within giraffes for effective conservation, including reintroductions and population management strategies. The findings also suggest that reproductive barriers between major giraffe lineages may have evolved more recently, as captive and wild hybrids have been documented. The study provides genomic resources that are crucial for maintaining genetic diversity across major lineages and sublineages of giraffes.