Abstract. Many horse populations suffered severe decreases in numbers in the last century; some, such as the Coldblood horse breeds drastically declined in their population size, while others could be saved at the last minute. It is important to evaluate the amount of genetic variability still present in those populations in order to develop conservation programmes. Furthermore, it is essential to construct phylogenetic trees and to establish the relationships among different horse populations in order to deepen our understanding of the evolution and domestication of the horse. In the past ten years microsatellite markers have been widely used to assess genetic variability within and between different horse breeds. Moreover, attempts have been made to evaluate the phylogenetic relationships of different horse breeds by comparing mitochondrial DNA (mtDNA) sequences. In this paper we give an overview of the latest major findings in studies based on horse microsatellite data and mitochondrial DNA sequences.