There are many horse breeds included in conservation programs around the world. The current populations of these breeds have often been derived from a small number of founders. The genetic structure of two endangered horse breeds – Silesian Noriker and Czech-Moravian Belgian was studied based on founder contribution analysis. Silesian Norikers are descended from 1235 founders and Czech-Moravian Belgians are descended from 2583 founders. The ef­fective numbers of founders and ancestors contributing to the current genetic pool were 69.42 and 22.32 for the Silesian Noriker breed and 43.33 and 23.32 for the Czech-Moravian Belgian breed respectively. Approximately 50 % of total genetic variation was explained by 31 founders with the greatest influence for the Silesian Noriker and 47 most influen­tial founders for the Czech-Moravian Belgian, with a maximum individual contribution of 8 % for Silesian Noriker and 14 % for Czech-Moravian Belgian. These results suggest that the genetic variability has decreased and without changes in breeding strategy, the genetic variability might continue to decline. The further expected loss of genetic variability in the populations can be minimized by increasing the number of descendants of low-represented founders.