In this study we analysed the genetic variability of the Austrian Haflinger horse population by use of pedigree analysis. For the analysis of inbreeding and genetic variability we defined three different reference populations which included active breeding animals with registered progeny in the main stud book. The mean inbreeding for 2.560 breeding animals between 1978 and 1985 (reference population 3, R3) comprised 6,34%, the effective number of founders was 43 and the effective number of ancestors was 18. In the following two reference populations (R2 1993 and 2000; R12008 and 2015) the genetic variability further decreased. The mean inbreeding increased from 8,83% in R2 to 11,92% in R1 and effective number of founders comprised 35 in R2 and 14 in R1, and the effective number of ancestors was 31 in R2 and 12 in R1. The gene pool of the actual Austrian Haflinger population consists of 6,9% Arabian genes, 1,7% Gidran genes, 1,8% Noriker genes, 58,6% genes from Original Haflinger founder mares (Ohast.), 24,1% genes from Haflinger horses, 0,01% genes from crossbred mares and 6,9% of genes go back to a Galician founder mare of the 19th century. Finally the decrease of genetic variability and the mean inbreeding increase of about 1% per generation in the Austrian Haflinger population shows, that in spite its worldwide distribution and the large international population size, it will be necessary to apply strategies from conservation genetics. In this context the major challenge will be the incorporation of founder contributions in small frequencies actually not being used in reproduction in order to increase the amount of alleles in the actual Haflinger gene pool.