Central Veterinary Laboratory of Algete (LCV) has been appointed as a referral center for the analysis of genetic markers and certification of techniques for the identification and genealogical control in horses, in order to guarantee the genealogies of the animals entered in studbooks (Royal Decree 662/2007). Since then, it has developed a working protocol covering all the steps to follow from the collection of samples in the field until receipt of the final results by the breeders? association. The methodology uses the most advanced and has established a series of checkpoints in order to detect any errors that may occur in both the sample collection and transmission of information that must accompany them for later analysis. The optimization methodology enables to process a large number of samples in a short time with great reliability in the results. The analysis that the samples are submitted includes 18 microsatellite DNA markers, amplified in a single PCR reaction, chosen from the list proposed by the ISAG (International Society for Animal Genetics). It also provides two additional panels composed of 8 and 22 new markers, respectively, which are used in cases where there is a need for increased capacity of exclusion or to conduct studies pedigrees with data from parents from other laboratories where use these markers, which is quite common in horse races where there is great movement of animals between countries.