Partition of the genetic variability, genetic structure and relationships among seven Spanish Celtic horse breeds were studied using PCR amplification of 13 microsatellites on 481 random individuals. In addition, 60 thoroughbred horses were included. The average observed heterozygosity and the mean number of alleles were higher for the Atlantic horse breeds than for the Balearic Islands breeds. Only eight percentage of the total genetic variability could be attributed to differences among breeds (mean FST approximately 0.08; P < 0.01). Atlantic breeds clearly form a separate cluster from the Balearic Islands breeds and among the former only two form a clear clustering, while the rest of Atlantic breeds (Jaca Navarra, Caballo Gallego and Pottoka) are not consistently differentiated. Multivariate analysis showed that Asturcon populations, Losina and Balearic Islands breeds are clearly separated from each other and from the rest of the breeds. In addition to this, the use of the microsatellites proved to be useful for breed assignment.
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