SummaryThe gene frequency differences of 18 alleles at five biochemical polymorphism loci were used in a 6‐breed comparison test between the Lipizzans from Austria, Czechoslovakia and Hungary, Haflinger, Noriker and Trotters, in an effort to establish their relationships. Phylogenetic analysis as proposed by Cavalli‐Sforza and Edwards was employed. The constructed clusters appeared to be in good agreement with the historical and geographical facts, reflecting, for example, the separation existing since over thirty years between the three Lipizzan breeds in Hungary, Czechoslovakia and Austria. The position of Haflinger and Noriker also conforms approximately with the historical dates of breed origins. In contrast, the positioning of the Trotters, which have a high percentage of French parentage, meets with some difficulties. The addition of two other loci with four alleles, applied to animals from three breeds, does not give any information beyond that of the first clust