Runs of homozygosity (ROH), which are contiguous homozygous fragments of DNA sequence without heterozygosity in the diploid state. Long ROH segments are supposed to be autozygous stretches originating from a recent common ancestor, while shorter ROH segments originate from distant ancestors. The main aim of this study was to investigate the existence and comparison of ROH islands across the genomes of Taurine (Angus, Fleckvieh, Brown Swiss) and Indicine (Nelore, Gir, Brahman) breeds. The term ROH islands is used to describe regions of the genome where many individuals of a population share ROH. We also compared ROH estimation using different software tools, e.g. cgaTOH, PLINK and SVS. We confirmed that small and long segments of ROH are present and abundant in the bovine genome and in some regions they are frequently observable even across unrelated individuals. Their size differed from 1 Megabase (Mb) to long segments spanning multiple Mb. We have also found some specific locations in the genomes in which ROH fragments were significantly conserved (ROH Islands/Hot spots) within and between the Taurine and Indicine cattle breeds. In addition, ROH Islands were observed to be in gene-rich portions of the genome. Even though the density of ROH patterns was always significantly different among the 3 software tools, there was a consensus as to the location of ROH islands discovered. Unique ROH patterns were found for each breed and between breeds, which was consistent with possible signatures of either artificial or natural selection. Since these patterns are an indication of common ancestry, either in the recent or remote past, these results could be beneficial for evolutionary studies as well as for fine mapping gene discovery studies. There is the possibility to use these ROH islands as surrogate markers in case-control experiments to see whether there is any relationship between them and recessive diseases or not. The same can be done for studying economic traits.