The characterisation of the small ruminant populations in developing countries will play a major role in the maintenance of the genetic resources as the basis for future improvement in livestock production. The present study aimed at morphological characterisation of the two main breeds of sheep in Ghana by assessing variation within and between breed populations using principal component and discriminant analyses. The two breeds were the Sahel and the Djallonke sheep of both sexes and of two groups namely, young (1 year old, consisting of 74 animals) and mature sheep (≥ 2 years old, comprising 219 animals). The analysis of variance revealed significant (P < 0.05) differences in the morphological traits of the Sahel and the Djallonke sheep breeds with higher values recorded for the former. Sexual dimorphism was in favour of male animals in all the morphological traits examined. Mature animals also had comparative advantage over the young. Two principal components were extracted to discern the structure of the two genetic groups. The most discriminating traits between the two sheep breeds were rump height, height at withers, neck girth and pin-bone width. Mahalanobis distance between the two genetic groups was 5.723 (P < 0.0001). The developed discriminant functions clearly discriminated and classified the Sahel and the Djallonke sheep into their breeds of origin, thus yielding 100, 93.4 and 90.4 % accurate classification for the rams, ewes and the overall sheep population, respectively. The present approach would greatly help in establishing management and conservation policies for the sustainable production of the two Ghanaian sheep breeds.