Spanish Churra and Ojalada sheep breeds have white wool and characteristic dark patches in the face (around the eyes and muzzle, and on the ears and nose) and distal parts of the body (mammary gland, genitals and legs). Crosses of Churra sheep with breeds missing these dark patches (e.g. Assaff or Awassi) suggest an additive inheritance for the dark patching phenotype with the first generation cross individuals showing patches that are less intense, in colour and extension, than those of Churra pure-breed individuals. We used a genome-wide ovine SNP array for mapping this trait, assuming that the same variant or variants are responsible of the dark patching phenotype in Churra and Ojalada breeds. Within the framework of the Sheep HapMap project a total of 172 ewes from four different breeds were genotyped with the Ovine SNP50BeadChip (Illumina, Inc). In addition to the two breeds under study, Churra (n = 100) and Ojalada (n = 24), the genotyped population included animals from two other Spanish breeds of white colour and without dark patches, Castellana (n = 24) and Rasa Aragonesa (n = 24). From the 54,241 SNPs genotyped, and after a quality control (QC) of genotypes, a total of 48,361 SNPs were subjected to an association analysis (124 dark patched individuals vs 45 controls). A case-control genetic association analysis revealed the most significant association on sheep chromosome 2, with the most significant associated marker showing a Bonferroni adjusted p-value = 4.28149E-70. Other highly significant associations were found on chromosomes 13 and 19. Further research efforts will be focused on the genomic region that harbours the SNPs showing the highest association with the studied trait.