The publication presents data on the genetic structure and differentiation of populations in large and small ruminants during breed formation. The objects of the study were aboriginal sheep of the Tsushka breed, the Moldavian type of Karakul sheep, the Moldavian wool-meat-milk type of Tsigai sheep, the local wool-milk type of Tsigai breed, populations of Holstein cows (Dutch breeding origin), and the Moldavian type of Black and White cattle. It was found that the isolating character of differentiation (D = 0.13; 0.15) was found in the populations of sheep of the Moldavian type of Karakul and in the indigenous breed of Tsushka, as well as in the local wool-milk type of Tsigai breed and in the Moldavian wool-meat-milk type. The most heterogeneous and remote (D = 0.24) were the populations of indigenous sheep of the Tsushka breed and the local wool-milk type of Tsigai breed, as well as the population of the Moldavian type of Black and White cattle (D = 0.23) relative to the populations of Holstein cows of the Holland selection.