The relationship between haemoglobin polymorphism and haematological pattern were studied in Gentile di Puglia, the Apulia Merino native breed. In a sample of 292 individuals, on five different farms, alpha- and beta-globin genetic polymorphism was investigated. A remarkable polymorphism was detected especially at alpha-globin gene where the variations concerned both the quality of the gene product and gene expression. Triplicated and quadruplicated alpha-globin genes were observed in 8.6% and 1.2% of the alpha-haplotypes respectively. At beta-globin (HBB) locus, predominance of HBB(B) allele was found in all flocks, while HBB(A) overall frequency was around 11.2%. Moreover, the effect of genotypes at globin systems on haematological data was evaluated on 289 animals. A significant effect was detected for HBB locus on haematocrit (HCT) and mean corpuscular volume (MCV), with decreasing HCT and MCV for decreasing number of HBB(A) alleles in the genotype. The opposite trend was observed for mean corpuscular haemoglobin concentration. The advances presented by this paper give reasons for inferring that BB genotypes can be expected to be more resilient to climatic stress and to local parasites.