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Strong genetic structure has prompted discussion regarding giraffe taxonomy, 1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa). 4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, F ST , among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations. [Display omitted] • Giraffes show exceptional genetic structure despite lack of physical barriers • Giraffes have a complex evolutionary history, with high levels of gene flow • Reticulated giraffes are a hybrid lineage • For effective conservation, diversity within giraffes needs to be taken into account Giraffes consist of four major lineages, which show strong divergence despite being geographically close. Following analyses of whole genomes from 90 wild giraffes from throughout their range, Bertola et al. show that the evolutionary history of giraffes is complex and marked by major gene flow, in particular affecting Reticulated giraffes. [ABSTRACT FROM AUTHOR]