Simple Summary Ecuador is considered a biodiversity reserve in which 951 native freshwater species of fish are recognized. Most of them have not been characterized and are endemic, inhabiting fragile ecosystems and presenting an endangered situation. In this work, chame was morphostructurally characterized; sex and production systems (cultured and wild) were considered factors of variation. This research represents a first step towards the development of breeding and conservation plans for this native zoogenetic resource. Abstract Ecuador, a country exhibiting large developments in fish farming, has a great variety of freshwater native fish. Among these fish is the Dormitator latifrons or chame, which has characteristics that make its farming prone to occur at a quite-developed stage. However, morphological characterization is required to establish a conservation program. In this study, 300 chames were captured in the Manabi province (Ecuador) to analyze their morphostructural model and to evaluate the effects of sex and the production system through multivariant techniques. The fish from the farm presented morphological measurements that were statistically ( p < 0.05) higher than those of wild fish. Males were taller, longer, and wider than females, although the differences were not significant ( p > 0.05). The percentage of correct adscription was 84%, with larger errors in wild fish. The morphostructural model had a high homogeneity, with 89.95% significant correlations ( p < 0.05), and wild male and female fish were more homogeneous. The farm fish were larger because of the higher food availability. Moreover, the species exhibited sexual dimorphism, although there were no great differences in the morphometric measurements. This study shows the great biodiversity that naturally exists in Ecuadorian rivers. Therefore, it is of great interest to develop a chame breeding and conservation program.