Based on geometric morphometrics and discriminant analysis, the percentage of silverside Odontesthes hatcheri and Odontesthes bonariensis individuals identified by a taxonomic key and misclassified by discriminant analysis was obtained and a negative correlation between the percentage of misclassified individuals of O. hatcheri and the distance to the nearest hatchery stocking silversides was found, suggesting a genetic introgression. Morphological analyses between species, between populations and within populations pointed to the same anatomical structures, suggesting a nested variation related to environmental cues such as availability of littoral shelter. The dependence between the cephalic morphology of O. hatcheri and body size would be in agreement with the trophic niche shifts of the species. Introgression adds a new threat to the already observed decline of populations of O. hatcheri and suggests that this species deserves particular consideration in terms of conservation guidelines.