A truss network was applied to analyze morphometric differentiation among three wild populations of Hoplias microlepis, captured in three different sites from two habitats of Guayas Hydrographic Basin: Daule-Peripa dam, Quevedo and Babahoyo rivers. This study can help to deepen to the knowledge of the species adaptation to different environments and highlights some factors which may be helpful for future management and conservation of the freshwater resources of Ecuador. A sample of 225 adult fish were collected, 49 morphometric characteristics and 6 meristic counts were analyzed, and a statistical model was built through multifactorial discriminant analysis. The standard length of Hoplias microlepis was 32.14 cm, total length 37.82 cm and sexual maturity index 4.39. The Hoplias microlepis with the greatest weight, length and sexual maturity index were in the dam where the food availability is better, and the fishing pressure is lower. Finally, the cluster analysis grouped the fish from the rivers in cluster 1 and those from the dam in cluster 2, being samples of dam clearly distinct from rivers, probably due to differences in the habitat condition. Fish body condition and morphological variation at different sites may be useful indicators for both, habitat disturbance and consequently its conservation, and the sustainability of fishery management plans.