Allelic frequencies at 12 loci (five blood groups: C, D, K, P, and U; and seven protein polymorphisms: Al, A1B, Es, Gc, Hb, PGD, and Tf), are given for two Brazilian horse breeds: Mangalarga Marchador and Mangalarga. The high genetic identity value found (96.0%) is consistent with their common origin, although, at some point of the development of Mangalarga Marchador, Mangalarga separated from the original stock. The expected average heterozygosity was higher in Mangalarga Marchador. The populations presented genetic differentiation, as shown by the statistically significant value of F ST . The nonsignificant F IS values showed that there was no appreciable consanguineous mating in any of the two populations. Exclusion probability calculated for the 12 loci was 87.0% and 86.5% for Mangalarga Marchador and Mangalarga, respectively. No genetic equilibrium was observed in the A1B, Tf, and Es loci of Mangalarga Marchador. The frequencies of blood factors A, Q, and T were calculated.