ABSTRACTThis study was undertaken to evaluate some selected productive traits and relationship between three genetic groups of cattle (Bunaji, Friesian X Bunaji cross and Sokoto Gudali) using blood biochemical polymorphism. A total of 150 cows consisting of 50 per genetic group was randomly sampled from the (NAPRI) cattle herd and used for the study. The selected productive traits evaluated include body height: (BW) in Kg, body length in cm (BL) height at withers (HW) in cm, chest width (cw), heart girth (HG), rump width ((Rumw) teat length in cm (TL), rear udder height (RUH) udder circumference (UC), total milk yield (TY), average daily milk yield (ADY) and lactation length in days (LL). Blood biochmeical parameters, namely Haemoglobin, Transferrin and carbonic anhydrase were evaluated for genotypic and alletic frequencies of these blood protein polymorphism and their impacts on productive traits, correlated analysis of the measured trait, principal component analysis of the variables, stepwise linear regression and multivariate analysis involving discriminant genetic distance and classification components between breeds were all computed. Results showed that BW and other measured traits differed significantly (P<0005) among the genetic groups BW and BL were higher in the Friesian X Bunaji than the Bunaji and Sokoto Gudali which showed no significant (P>005) difference for these traits. The haemorglobin1ocus revealed overall allelic frequencies of 0.44 and 0.13 for HbAA and HbBB respectively. Low frequencies of alleles (0.20, 0.20 and 0.40) were observed in the Bunaji, Friesian X Bunaji and the Sokoto Gudali respectively. In the transferrin locus, only the A and B alleles were observed with overall frequencies of 0.16 and 0.09 respectively. Low genotypic frequency of 0.04 for AA was obtained in the Sokoto Gudali while the Bunaji and the Friesian X Bunaji recorded frequencies of 0.30 and 0.12 respectively. In the carbonic anhydrase locus, only the F and S alleles were observed with the overall frequencies of 0.17 and 0.23 respectively. Both the Tranferrin and Carbonic Anhydrase locus were not in Hardy-Weinberg equilibrium for the studied population. Significant (p<0.05 differences were obtained in all body and milk production traits measurements of the three studied population indicating clear genetic group distinction. It was noted that the Sokoto Gudali was superio to the Bunaji in most of these traits though the Sokoto Gudali is a relatively poor milker than the Bunaji. Study of blood protein polymorphism and productivity indicated significant (p<0.05) influence of the haemoglobin, transferrin and carbonic anhydrase on both body and milk viii production traits. Correlated studies were observed to be very significant between variables in the pooled analysis by majorly insignificant for individual genetic groups, also estimates were generally low though ranging from 0.87 - 0.84. Principal component analysis observed to show factors ranging from 3 in the pooled data to 5 in the Bunaji and 6 in the Friesian X Bunaji and Sokoto Gudali genetic groups. Generally communalities ranged from 0.31 - 099 whils proportion of variance accounted for by factors were 47% in the pooled and Bunaji and 58% in the cross breed and Sokoto Gudali. Multivariate analysis indicated TY, CW, ADY, RUH, LL, Rumwi, UC, TL and HG as the most discriminating variable among the genetic groups. Their respective partial R2 and F values were (0.84, 0.58, 0.22, 0.150.13, 0.09, 0.08, 0.15 and 0.04) and (2278.64, 613.22, 123.85, 81.12, 65.12, 43.02, 37.10, 79.68 and 16.52) with high significant value of (p<0.0001). Genetic distance among the genetic groups revealed high Mahalanobis value (3.94 - 4.95) between the Bunaji and Sokoto Gudali and Friesian X Bunaji and Sokoto Gudali. The Highest proper classification (84%) was in the Sokoto Gudali and it indicated greater genetic group homogeneity. However, multivariate studies clearly indicated manifestation of gene introgression across genetic groups through indiscriminate cross breeding. Perhaps as evidenced by the high levels of misclassification in the Bunaji, Friesian X Bunaji and Sokoto Gudali. There is a need for generic study using protein and DNA microsatellite makers to compliment the results arisen from morphometric differentiation of the two most popuous Nigerian breeds of cattle in the NAPRI herd.