Samples of 72 animals from three flocks were analysed using nine microsatellites in order to evaluate the connection between existing populations of Cikta sheep, an indigenous breed in Hungary. Cikta was a well-known and popular breed until 1960-70. Nearly 30,000 animals were recorded in 1947 whereas the breed came close to extinction in 1975 when only 112 animals remained and genetic preservation programme was launched. Today's population is considered stable with approximately 1000 record animals. Fluorescent-labelled oligonucleotides and fragment length analysis was applied for microsatellite genotyping. Overall, observed and effective allele numbers were 5.63±1.71 and 3.76±1.10, respectively. Mean Fis (-0.18±0.12) and Fit (-0.13±0.11) values indicated heterozygous excess. Considerably low mean Fst (0.04±0.03) and discriminant analysis revealed lasting effects of the 1970s bottleneck as three analysed populations showed slight genetic differentiation. Three of the nine microsatellites significantly (P<0.05) deviated from Hardy-Weinberg equilibrium, namely BM8125, CSSM47, and MAF214. Results can be applied in mating plans to maintain existing diversity in the breed.