Marwari sheep breed is the main constituent of the migratory sheep flocks in the Rajasthan, India. The purpose of this research was to use pedigree data to evaluate population structure and genetic variability in a closed flock of Marwari sheep in Rajasthan, India. Pedigree information of 11,659 sheep lambed from 1981–2020 (39 years) in the closed flock of Marwari sheep reared at ICAR-CSWRI-ARC, Beechwal, Bikaner, Rajasthan, India were included in the analysis. Lambs born during 2017–2020 were considered as reference population. The mean of maximum generation (MG), complete generation (CG) and equivalent complete generation (EqG) was 9.12, 2.75 and 5.35, respectively. The completeness of pedigree was 92.70 % (1st generation), 83.03 % (2nd generation) and 73.79 % (3rd generation). Average inbreeding coefficient for animals in the whole and reference populations was 1.49 and 2.40 %, respectively. The average relationship coefficient for whole and reference population was 2.51 and 3.34 %, respectively. Mean generation interval (GI) were 3.5 and 3.3 years for whole and reference population. The realized effective population size was 87.17 for whole population. Effective numbers of founders (fe), ancestors (fa) and founder genome (fg) was 80, 46 and 16.76, respectively for reference population. The fe/fa ratio in the reference population was 1.74, indicating that bottlenecks had occurred. The genetic contribution of the 16 most powerful ancestors represented half of the genetic variability in the reference population. The findings showed that there were proofs of bottleneck and genetic drift however, there was also considerable genetic diversity present in the population. The continuous flow of genes has contributed to the maintenance of genetic variability in the closed flock reflecting that management was in right direction in the Marwari sheep nucleus flock.