Coat color and especially the leopard complex spotting (LP) is a central breeding objective in the Austrian Noriker horse. Being part of the breeding program, the breeding of leopard complex horses is characterized by a 350 years lasting continuity and by a specific nomenclature which is different to the American LP nomenclature. In this study we analysed and discussed the differences between the two systems on basis of image analysing methods and genotyping for the actually known LP-associated alleles LP (ECA1 g. 108 297 929_108 297 930 ins1378) and PATN1 (SNP ECA3:23 658 447T > G in 3'). From 111 LP horses (43% of actual breeding population) the white pixel percentage (equivalent to white pigmentation areas on the coat) was derived and tested for differentiation between the main LP categories (leopard, few spot, flecked with grey, spotted blanket) used in the breeding program of LP horses. Each of the categories differed significantly from each other. We further performed a longitudinal study including 24 horses where we measured the white pixel percentage over time in order to study depigmentation process associated with increasing age. Within this sample we identified two groups: variable and invariable LP horses, whereas for the category flecked with grey and leopard horses born with a well-marked leopard pattern, no loss of pigmentation which is due to increasing age could be identified. The white pixel percentage of the 24 genotyped LP horses belonging to the categories leopard, spotted blanket and flecked with grey, ranged from 12 to 88% and all of them had the genotype LP/lp PATN1/-. Thus the phenotypic variation could not be explained by the genotype. In this study we could show, that the LP-classification system implemented in the Noriker breeding program, the selection towards a well-marked black leopard, and the rotation-mating of LP horses with solid colored horses, are adequate instruments to increase the proportion of LP/lp animals and the frequency of the PATN1 allele in the population. As a consequence the two different classification methods also reflect differing phenotype frequencies within the breeds Noriker and Appaloosa.