Abstract <p>In the present study, the consolidation of horse breed groups was assessed using the microsatellite marker fragment analysis. Interbreed and intrabreed genetic distances were used as key indices. Intrabreed genetic distances were calculated by using the inverse of an identity-by-state (IBS) matrix. The level of genetic differentiation between populations was determined using the <i>F</i>_st method. Factory-bred and indigenous horse (<i>Equus caballus</i>) breeds, common in Russia and Europe, were used as model objects. An isolated horse population inhabiting Vodny Island located in the Rostovsky State Nature Biosphere Reserve (Rostov oblast) served as a control group, characterized by minimum genetic distance values typical of isolated populations. Randomized samples, including one random specimen from each studied breed, were artificially created to represent the group with maximum diversity. The results of the study revealed statistically significant differences in genetic distances (Dist(IBS)) and the fixation coefficient (<i>F</i>_st) between horse breeds and groups that differ in their breeding status.</p>