The Aosta cattle breeds have a key role in the economy of the Aosta Valley. In addition to the meat and milk production these autochthonous breeds are important for their cultural value, and for their role in the maintenance of the mountain environment. The knowledge of their genetic makeup represents a fundamental asset to managing the reproduction of the population in order to maintain the existing genetic diversity and, as a possible input, to apply genomic selection in a small population. A total of 3195 Aosta cows were genotyped with the GeneSeek Genomic Profiler® (GGP) Bovine 100K by Neogen in the framework of the DUALBREEDING-2 project. The Aosta Black-Chestnut and Chestnut-Herèn resulted to be a unique population. The Aosta female population had shorter ROH than bulls and shared ROH_islands that harbour adaptative and functional genes. Allele frequencies of major genes highlight the possibility for selection for both milk and meat quality variants and that the Aosta cattle population is free from the known Mendelian inheritance diseases found in cosmopolitan breeds (e.g. BLAD, CVM, HCD).