We evaluated the influence of areas with dissimilar upwelling intensity along the Humboldt Current System on the morphological variation of the economically important sea silverside Odontesthes regia by using geometric morphometric (GM) and meristic data of populations sampled off Northern Peru, Central Peru, Southern Peru-Northern Chile, and Central-Southern Chile (CSCH). Multivariate analyses of variance, a UPGMA tree, and discriminant analyses of meristic counts separated CSCH individuals, which had slightly higher numbers of gill rakers and radius of the anal fin. Permutation tests and canonical variate analyses of GM data distinguished all populations and highlighted deformations in the head and fins. Variations in GM and meristic analyses were significantly correlated with values of the sea surface temperature and surface chlorophyll-a concentrations. Morphological differences among populations might be associated with the spatial coastal upwelling dynamic of the Humboldt Current System, which highlights the role that this system plays in relation to the phenotypic variation of fish.