Morphological variation between Muscovy ducks from the guinea savannah and rainforest zones of Nigeria was examined using multivariate discriminant analysis. Data comprised eight morphometric traits measured in a total of 435 adult ducks randomly selected in the two agro-ecological zones. Common descriptive statistics showed that ducks from the rainforest zone had higher (P< 0.05) body weight, foot length and thigh circumference, while their guinea savannah counterparts were longer (P< 0.05) in the neck. Stepwise discriminant analysis indicated that foot length, neck length, thigh circumference and body length were more effective in discriminating between the duck populations. The low Mahalanobis distance of 3.39, as revealed by the canonical discriminant analysis, is an indication of high gene flow between ducks from the two agro-ecological zones. The cluster analysis also revealed the homogeneity of the genetic identity of the duck populations. The present information will be the basis for further characterization, conservation and sustainable genetic improvement strategies for indigenous ducks.