This study describes the results of molecular screening in the Agerolese cattle breed from southern Italy, which constitutes an economical source and contributes to the regional biodiversity. Integrated electrophoretic, chromatographic, mass spectrometric, and DNA sequencing procedures were used to qualitatively and quantitatively evaluate globin chain polymorphism in a population of animals from different farms. In addition to α-, β A -, and β B -globin-bearing animal phenotypes, our data demonstrate the occurrence of individuals characterized by the presence of a novel α-globin variant, whose primary structure differs from the normal counterpart for the p.Ala27Thr substitution. The SNP c.79G>A located at the exon 1 of the HBA2 gene is responsible for this amino acid change and it represents a third example of α-globin gene polymorphism observed in Bos taurus. This phenomenon was ascertained only in two Mediterranean breeds from southern Italy and highlights the uncommon occurrence of α-globin variants in this geographical region, similarly to what has already been described in goat and human.