The population variability of three breeds of Nigerian sheep was investigated using multivariate discriminant analysis. The sampled populations comprised mature 331 Yankasa, 296 Uda and 166 Balami sheep kept by traditional farmers in northern Nigerian. A total of ten morphological traits (withers height, rump height, body length, face length, rump length, tail length, chest circumference, head width, shoulder width and rump width) were collected on each animal. The univariate analysis revealed that the body measures of Balami sheep were significantly larger (P<0.05) than others with the exception of tail length. Uda sheep also had higher mean values (P<0.05) than their Yankasa counterparts in all the morphological traits analysed. However, the stepwise discriminant analysis revealed that head width chronologically followed by tail length, chest circumference and body length were more discriminating in separating the three sheep populations. The Mahalanobis distance of the morphological traits between Yankasa and Balami sheep was longest (4.83) while the least differentiation was observed between Uda and Yankasa sheep (1.79). Nearest neighbour discriminant analysis showed that most Balami sheep (61.45%) were classified into their source genetic group. While 41.22% of Uda sheep were misclassified as Yankasa sheep, 35.35% of Yankasa were wrongly assigned as Uda sheep, showing the level of genetic exchange that has taken place between the two breeds overtime. The present phenotypic information could be complemented with genetic analyses; and serve as a basis for designing appropriate conservation, breeding and selection strategies for Nigerian sheep.