Long consecutive homozygous genotype segments, runs of homozygosity (ROH), are a result of parents transmitting identical haplotypes, which can be used to estimate autozygosity. Based on 612K single-nucleotide polymorphisms, we computed three ROH parameters (genome length covered by ROH, SROH; number of ROH, NROH; and autozygosity, FROH) to investigate different scenarios in contemporary horse breeding: limited census (Bosnian mountain horse), conservation breeding (Posavje horse), and selection within closed studbook (Haflinger). The ROH parameters revealed well-defined differences between breeds. SROH was highest in the Bosnian mountain horse with 296.32 Mb, followed by the Haflinger sample (SROH = 270.35 Mb) and the Posavje sample with 192.68 Mb. The highest number of ROH segments (ROHs) was observed within the Haflinger sample followed by the Posavje sample. FROH ranged at a population level from 8.59% in Posavje, over the Haflinger (mean FROH = 12.05%) to 13.21% in the Bosnian mountain horse breed. Bottlenecks were detected for Bosnian mountain horse and Haflinger, whereas for the Posavje, a positive effect of the conservation breeding program was documented. Investigating the distribution of ROHs across the genome, we detected four common ROH islands on equine chromosomes ECA 6, ECA 11, and ECA 17, which were present in all breeds. On breed level, the Bosnian mountain horses contained 10, the Posavje, four, and the Haflinger, 11 distinct ROH islands (containing the MC1R locus on ECA 3). With this analysis, we were able to compare genomic levels of inbreeding between breeds differing in management, pedigree completeness, and genes under selection. •ROHs firstly identified for the breeds Bosnian mountain horse, Posavje, and Slovenian Haflinger.•Characterisation of genomic inbreeding, bottleneck situations, and population history.•Detection of ROH islands, which suggest distinct genetic regions exposed to selection.•Comparison of inbreeding in breeds differing in pedigree length and population fragmentation.