A recent work investigating genetic origin, admixture and population history of primitive European cattle highlighted, by using genome-wide single nucleotide polymorphisms, zebu gene flow in the Balkan and Italian Podolic cattle populations. Haemoglobin protein polymorphism analysis in Italian breeds highlighted the presence of zebuine markers in both Italian Podolic and Alpine Grey cattle. Based on the above evidences, we here specifically look for genomic regions of zebuine ancestry in a different dataset of 50K genotypes from Mediterranean breeds including 29 Marismena (Spain); 30 Bazadaise and 30 Gasconne (France); 24 Alpine Grey, 97 Piemontese, 51 Chianina, 5 Marchigiana, 121 Romagnola, 24 Podolica, 24 Modenese, 30 Reggiana, 30 Cinisara and 30 Modicana (Italy); 24 Guelmoise (Algeria); 24 Cika (Slovenia), 43 Illyrian Mountain Buša (Albania). Additional taurine and zebuine breeds from previously published studies are also included in the analyses. Special emphasis in genetic analyses is also given to the identification of genomic regions potentially associated with a phenotypic trait observed in several taurine breeds as well as in some zebuine breeds, characterized by calves having a fawn coat at birth, while turning to various shades of grey in adult animals. The obtained results contribute to a better characterization of history and genetic structure of Mediterranean cattle breeds.