We have studied the genetic variability and relationships of four endangered Spanish equine populations for meat production using mitochondrial DNA (mtDNA) (41 horses, 30 of them belong to Burguete (BUR), Hispano Bretón (HB) and Agrupación Hipermétrica del Pirineo (AHP) populations and the other 11 samples belong to Jaca Navarra (JAC) breed. Fifteen haplotypes were found and 19 polomorphic sites were detected, eighteen of them were parsimony informative sites and the other one was a singleton. Haplotipic diversity (Hd) ranged from 0.758 of AHP to 0.993 of BUR breed. The average Hd value was 0.929 (SD = 0.016). The JAC breed presented the highest nucleotide diversity value (0.023). Most of haplotypes found have been shared by the four horse populations except haplotype 8 that only was presented by AHP populaton, haplotype 10 by BUR, the haplotypes 13 and 14 by HB and haplotype 15 by JAC breed. A clear group of horses belong to the same population were not shown. These results confirm the multiple maternal origin previously shown by other authors. However we have found haplotypes specific of each breed that is important to take in account in their conservation programmes.