Knowledge of both the genetic diversity and geographical distribution of animal genetic resources is a prerequisite for their sustainable utilization, improvement and conservation. The present study was undertaken to explore the current morphological variability within the sheep population in Benin as a prelude for their molecular characterization. From November 2018 to February 2020, 25 quantitative linear body measurements and 5 qualitative physical traits were recorded on 1240 adult ewes from the 10 phytogeographic zones that comprise the three vegetation zones of Benin. Fourteen morphological indices were calculated based on the linear body measurements. The collected data were first analyzed using multiple comparisons of least-square means (LSmeans), followed by generalized linear model (GLM) procedures, to explore the relationships among the measured morphometric traits and the 10 phytogeographic zones. Next, the presence of any genetic sub-populations was examined using multivariate analytical methods, including canonical discriminant analysis (CDA) and ascending hierarchical clustering (AHC). Univariate analyses indicated that all quantitative linear body measurements varied significantly (P<0.05) across the phytogeographic zones. The highest values (LSmean± standard error) of withers height (68.3±0.47 cm), sternum height (46.0±0.35 cm), and rump height (68.8±0.47 cm) were recorded in the Mekrou-Pendjari zone, the drier phytogeographic zone in the North, whereas the lowest values, 49.2±0.34, 25.9±0.26, and 52.0±0.35 cm, respectively, were recorded in the Pobe zone in the South. Multivariate analyses revealed the prevalence of four distinct sheep sub-populations in Benin. The sub-population from the South could be assimilated to the short-legged and that from the North to the West African long-legged sheep. The two other sub-populations were intermediate and closer to the crossbreeds or another short-legged sub-breed. The proportion of individuals correctly classified in their group of origin was approximately 74%. These results uncovered a spatial morphological variation in the Beninese sheep population along a South-North phytogeographic gradient.