In order to ascertain the effects of past breeding decisions on the genome we studied three Haflinger subpopulations representing the old-type (South-Tyrol), an intermediate type (Slovenia) and the modern type (Austria) by means of a high density 670k SNP genotyping array. High-resolution network analysis, FST- and Admixture analysis, underlined the high genetic distance of the South-Tyrolean Haflinger in relation to the other two samples. This differentiation was also highlighted by ROH analysis, where 15 out of 19 ROH islands were privately detected within the respective subpopulations. Common ROH islands among the three subpopulations were found on ECA3 and ECA7 containing inter alia genes related with behaviour (JPH3) and coat color (MC1R). The South-Tyrolean and the Slovenian (below threshold) sample exhibited a ROH island on ECA1 containing OCA2, which may be involved in the breed-specific sorrel phenotype of the Haflinger. Body size associated SNP genotypes at the LCORL/NCAPG locus revealed a fixation for the small body size associated alleles for all collected samples, whereas for SNPs associated with height at withers at the ZFAT locus a genomic shift towards taller horses was detected in Austrian Haflinger, which were exposed to a high selection pressure for this trait throughout the past four decades.