The main objective of the study was to determine the genetic diversity in sire lines of two Czech endangered breeds (populations in the context of a currently conducted conservation program) – Silesin Noriker (SN) and Czech-Moravia Belgian (CMB) and one open breed – Noriker (N). A total of 2,202 animals of 24 lines were considered. Pedigree analyses were carried out for the whole population registered in the studbooks of analyzed breeds. Differences among the sire lines were evaluated using genetic distances and cluster analysis. One gene cluster comprised CMB sire lines, while the third cluster included the sire lines of the N breed. In the second cluster were combined sire lines from the SN and N breeds. The minor genetic differences between sire lines of the SN and N were observed in the second cluster. These results showed that a revision of the breeding strategy is suggested especially between SN and N breed.