Diplostomum species are economically important worldwide due to their metacercariae which parasitize the eyes of fish, in both natural and aquaculture systems. However, their striking morphological similarity, especially at the metacercarial stage, makes species separation difficult. Three closely related diplostomid metacercariae, namely Diplostomum mashonense (type 3), Tylodelphys sp. 1 and 2 (type 1 and 2, respectively), coexist in the cranial cavity of the catfish, Clarias gariepinus from Mindu dam, Lake Victoria, Msimbazi, Ruvu and Kilombero rivers. The morphometrics of these three species were analysed by discriminant function analysis to investigate the degree of variation among the populations from the five localities sampled. The first canonical functions for all visual examination plots accounted for over 50% of the between-group variability. The observed differences were mainly from measurements associated with length, indicating that these measurements are important in the description of population characteristics. Visual examination of the samples along the canonical functions showed a clear between-population differentiation. The overall random assignment of individuals into their original groups was high (97%). These extensive morphometric variations introduce doubt about the reliability of measurements in the determination of species in these trematodes, as they may lead to misidentifications.