Based on pedigree information, the population structure, within-breed genetic variability and causes of genetic variability losses in Wallachian sheep (WS), and Sumava sheep (SS) were studied. The maximum number of generations observed in both WS and SS was 16, and the equivalent number of complete generations 5.66 and 4.35, respectively. The average generation intervals were in WS and SS 4.33 and 4.72 years, respectively. A span of four years, 2015–2018, was used as the reference population (animals from the last generation). The average inbreeding coefficient and average relatedness coefficient were 5 % and 9 % for WS, while both were 3 % for SS. The rate of the inbreeding coefficient was 0.5 % in WS and 1 % in SS. The effective number of founders, effective number of ancestors and effective number of founder genomes were 104, 50 and 22.8 for SS and 39, 21 and 10.28 for WS. The effective population size based on an increase in the inbreeding coefficient and computed based on average coancestry were 50.61 and 64.5 in WS and 99.56 and 166.14 in SS. These results indicate a low value of genetic diversity in Wallachian sheep. The loss of variability was caused by the bottleneck effect and partly also genetic drift and the unequal contribution of the founders. © 2020 Elsevier B.V.