Abstract. Microsatellite analysis was used to estimate the genetic origin, differences, relationship within 10 Hungarian Tsigai populations. The number of alleles was 262 at the 16 examined locus. Fifteen population specific alleles were detected. The mean number of alleles detected per locus ranged from 4.3 (OarAE119) to 11.9 (MAF70). Genetic distance values were calculated from Nei’s minimum genetic distance (DA) formula. Phylogenetic tree was constructed using UPGMA algorithm. The results indicated that the genetic difference was negligible between the following populations pair-wise: two Hungarian indigenous populations (Kardoskút1-IN and Kardoskút2-IN); the Hungarian indigenous population Soltszentimre-IN and the Milking Tsigai population Akasztó-ZO; the Hungarian indigenous population Csanádpalota-IN and the transitional type population Makó-Rákos-TR. Microsatellite genotyping prooved to be efficient tool for examing the genetic relationships among Hungarian Tsigai populations.