Abstract. The genetic relationships among the indigenous Hungarian Mangalica swine breeds in farms at different geographical locations have been studied by ten microsatellite markers (S0005, S0090, S0101, S0155, S0355, S0386, SW24, SW240, SW857, SW951), in order to characterise the population and to give sound scientific basis for management practices. The work hypothesis – that Mangalica individuals form just one unpartitioned population – has been rejected. The estimated value of clusters in population is three and it is in content with the history of the breeds. The estimated distances (Ds, Da, Fst) were the smallest between Swallow-Belly and Blond, while the Red showed the largest genetic distance from the previous two breeds. This approach proves the existence of distinct populations and can be used for assignment of individuals with high probability value (in the range from 0.83 to 0.91) to the different Mangalica breeds if required.