Increasing the fertility of sheep remains one of the crucial issues of modern sheep breeding. The Kazakh meat-wool sheep is an excellent breed with high meat and wool productivity and well adapted to harsh conditions. Nowadays, runs of homozygosity (ROHs) are considered a suitable approach for studying the genetic characteristics of farm animals. The aims of the study were to analyze the distribution of ROHs, describe autozygosity, and detect genomic regions with high ROH islands. In this study, we genotyped a total of 281 Kazakh meat-wool sheep using the Illumina iScan system (EquipNet, Canton, MA, USA) via Ovine SNP50 BeadChip array. As a results, a total of 15,069 ROHs were found in the three Kazakh meat-wool sheep populations. The mean number of ROH per animal across populations varied from 40.3 (POP1) to 42.2 (POP2) in the category 1+ Mb. Furthermore, the number of ROH per animal in ROH were much higher than ROH and ROH in the three sheep populations. Most of individuals had small number of ROH. The highest and lowest genomic inbreeding coefficient values were observed in POP2 and POP3, respectively. The estimated F presented the impact that recent inbreeding has had in all sheep populations. Furthermore, a set of interesting candidate genes (, , , , , , , , , and ), which are related to the productive traits, were found. Collectively, these findings will contribute to the breeding and conservation strategies of the Kazakh meat-wool sheep breed.