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Species divergence under geographically varying selection across disparate habitats has intrigued ecologists for decades. The Lake Chilwa inland drainage basin in Malawi has historically undergone wild water-level oscillations, sometimes being split into various sub- basins. Hydrological regime shifts may drive morphological variance in fishes. Although many scientists have studied fishes of this basin, we know little about the potential effects of its stochasticity on its ichthyofauna. Traitbased approaches are useful for detecting phenotypic changes among different populations. We used morphometric analysis to assess morphological disparities among three allopatric populations of Enteromius paludinosus, a fisheries-dominant cyprinid of this basin. Specimens from its three inlet rivers were measured on 18 traits and the data analysed using principal component analysis, the Welch-F test and t-tests in the Palaeontological Statistics package. Two river populations were clearly separated along seven traits: post-anal distance II, post-dorsal distance I, post- dorsal distance II, post-anal distance I, pre-anal distance, pre-pelvic distance and predorsal. This divergence may be related to different abiotic selective pressures in their unique habitats, perhaps mediated by adaptive phenotype switching and incongruent growth trajectories. More eco-morphological studies in this basin may fully unravel the link between its wild hydrological fluctuations and the eco-evolutionary dynamics of its fishes.