The Czech Republic is a small European country but it is a homeland for several dog breeds. In total, there are six Czech breeds. This is a first study that compares three of these breeds, Czechoslovakian Wolfdog (CSW), Chodsky dog (CHD) and Cesky Fousek (CF). CSW is a unique dog breed which originated from German Shepherds (GS) and Carpathian wolves (CW) in order to help protecting the Czechoslovakian borders. Experimental cross-breeding started in 1950’s using two CW females and two CW males and led to the CSW breed creation in 1989. The Chodsky dog´s history reaches back to 13th century when it was used as a guarding and sheep dog; however, after World War II the breed almost disappeared. In 1985, the regeneration process started when two standard females and three standard males were used for breeding. The breed of CF is the only Czech breed of pointer and it has a very complex history. In the past, when the breeds have not yet been properly established, it was often hybridized with other wire-haired breeds. In this study we assess genetic diversity of respective breeds regarding its history. In their genenome, we sought details of the domestication process, and the CSW breed is especially important for understanding interactions of genomes of wolves and dogs. This study was supported by Technical Agency of Czech Republic, project number TG03010020.