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ABSTRACT The objective was to verify the existence of lineages in the Mangalarga Marchador breed using microsatellites and to phenotypically characterize the lineages found using linear morphometric measurements taken at the time the animals were registered to be used as a tool for selecting individuals according to each breeder’s selection objective. The genotyping database contained 255,257 Mangalarga Marchador horses born between 2005 and 2021. In addition, a database was used with pedigree information on 622,299 animals born between 1952 and 2020 and a database of phenotypes assessed at the time of definitive registration of these animals, containing 303,248 animals born between 1950 and 2018. The databases used came from the Associação Brasileira dos Criadores do Cavalo Mangalarga Marchador. To verify the existence of genetic differences according to the lineages of the breed, a discriminant analysis of principal components (DAPC) and the Kruskall Wallis test were carried out to perform phenotypic characterization to compare the means of the morphometric measurements, both using the R software. The DAPC analysis showed the genetic differentiation of the Angaí and Herdade lineages in relation to the others. The Herdade lineage showed greater phenotypic differentiation when compared with the three separate genetic groups in this study, demonstrating that the animals of this lineage are smaller and more gathered and have higher scores for gait and morphology. When compared to the historically described Mangalarga Marchador lineages, the breed does not have so many genetic groups, separating it into just three groups (Angaí, Herdade, and General), and when compared to phenotypic characteristics, only the Herdade lineage stood out.