In a scenario of climate change and risk of losing biodiversity, the safeguard of locally adapted breeds and their genetic reservoirs assumes a key role. Furthermore, these breeds are linked to their rearing territory maintenance also through the nutritional, economic or social value of their products. This study focussed on the analysis of milk protein genetic variability of the Piedmontese, the most abundant beef Italian breed, and the Bara-Pustertaler breed, through the testing of individual milk samples by isoelectrofocusing. Allelic and haplotypes frequencies were analysed and the presence of rare variants (CSN1S1*G, 0.7%, and CSN2*C, 0.7%, in Bara and Piedmontese breeds, respectively) was detected. The analysed breeds showed allelic frequencies close to the one found in breeds with good cheesemaking aptitude, like the Italian Brown and Reggiana breeds (e.g. CSN2*B, 20.7% and 16.4%, and CSN3*B, 41,1% and 35%, in Piedmontese and Bara breeds, respectively), and are a good reservoir of alleles that are decreasing (e.g. CSN2*B) in Italian Holstein. Moreover, they have higher frequencies of interesting haplotypes (e.g. BA(1)B, 8% and 11.2%, and BA(2)B, 20.8 and 13.1% in Piedmontese and Bara breeds, respectively) that could positively influence composition, nutritional, and technological properties of milk. These breeds could be used to further investigate the effects of variants and haplotypes that could help support the evolution and the changing demands of the dairy sector.