Blood samples were collected from 324 goats belonging to the native Apulian breeds Garganica and Jonica; 60 Alpine goats were also sampled to serve as a comparison. Hemoglobin phenotypes were analyzed with isoelectric focusing in a pH range of 6.7-7.7. Heterogeneity of globin chains was evidenced both by AUT-PAGE and RP-HPLC. The primary structure of four alpha globins was analyzed by combined mass spectrometry approaches. Two of these globins had never been sequenced before. One was a new alpha variant, an allele of the HBA1A gene from which it differed for the mutation A26T and has been registered with a low frequency only in Apulian breeds; the other was a globin encoded by the HBA2 locus, whose primary structure was previously derived from the corresponding gene. The two alleles recorded at the HBA2 locus presented a different frequency in the three breeds but may be considered to be generally rather common. Notwithstanding the sample size no goat was found to exhibit HbA1B. The authors discuss their findings in the light of the results reported by other researchers and argue that, in spite of what had been inferred in pioneer works on goat hemoglobins, HBA1B is not a common allele.