During the development of the Sheep HapMap project, ewes from 6 breeds (Awassi, Merino, Poll Dorset, Romney, Scottish Blackface and Texel) were used to obtain the sequence of the ovine genome and look for variability. The Ovine SNP50BeadChip (Illumina) was then genotyped in 71 breeds, four of which were Spanish breeds. In some species (pig and cow) a bias has been described when testing a SNP Chip in different breeds. The aim of this study was to analyse this possible bias due to the sheep breed in the Spanish populations included in the Sheep HapMap project. For this purpose, we estimated for both, the breeds used in the Chip development and the Spanish populations the following parameters: MAF within and between breeds, gene diversity, individual heterozygosity and average proportion of alleles shared within population. The results obtained in Spanish breed were similar to those observed in the six breeds sequenced during the SNP-chip development. These findings support the value of Ovine SNP50BeadChip for genomic analysis in Spanish sheep breeds.