We studied the blood haemoglobin polymorphism and activity in relation to body morphology and milk traits in Nigerian indigenous breeds of cattle. A total of 150 animals, 50 per breed of the Bunaji, Friesian X Bunaji and Gudali were used to study the relationship between breeds. Variables measured were BW: Body weight (Kg); BL: Body Length (Cm); HW: Height at withers (cm); CW: Chest width (cm); HG: Heart Girth (cm); Rumwi: Rump width (cm); TL: Teat Length (cm); RUH: Rear Udder Height (cm); UC: Udder Circumference (cm); TY: Total Yield (Litres); ADY: Average Daily Yield (Litres/day) and LL: Lactation Length (days) and blood protein polymorphism of the Haemoglobin. Observed results showed overall frequencies of 0.62 (HbA) and 0.48 (HbB). Higher frequencies of the A allele (0.52, 0.54 and 0.68) were obtained respectively for the Bunaji, Friesian X Bunaji and Gudali cattle in the Haemoglobin locus. Study of blood protein polymorphism and productivity indicated significant (p<0.05) influence of the haemoglobin. There is a need for a genetic study using other proteins and at DNA level to compliment the results arisen from morphometric differentiation of the two most populous Nigerian breeds of cattle in the NAPRI herd.