A previous study based on a taurine pangenome uncovered a structural variant upstream of the KIT gene associated with depigmentation in white-headed cattle. In this study, we aimed to deepen our understanding of this region by analysing a collection of 80 genome assemblies from 20 different cattle breeds, including several not previously investigated. Using a combination of complementary approaches, we constructed a 2 Mb pangenome graph encompassing the KIT gene and the depigmentation-associated region to investigate the spectrum of structural variations within this region. Our analysis revealed a more fragmented structure than previously reported, mainly due to the inclusion of a larger number of assemblies (80 vs. 24) with varying sequencing technologies’ quality (CLR and HiFi). Despite this increased complexity, the identified structural variant’s alleles closely mirrored those reported in earlier study and depicting clear segregation of the population into two distinct groups. The first group includes breeds characterized by a white-headed phenotype and the second group contains all non-white headed breeds. We further validated this structural variant by aligning short-reads to the pangenome graph and genotyping several hundred animals for this structural variant. Our results provide new insights into the genetic mechanisms underlying head depigmentation in cattle and demonstrate the power of pangenome-based analyses for detecting trait-associated structural variations. This research was supported by funding from the Agreenium programme, with contributions from the Biosphera Graduate School, the ABIES doctoral school, the INRAE Animal Genetics division, and the INRAE GBOS team from the GABI department.