Phenotypic variation in organisms depends on the genotype and the environmental constraints of the habitat that they exploit. Therefore, for marine species inhabiting contrasting aquatic conditions, it is expected to find covariation between the shape and its spatial distribution. We studied the morphology of the head and cephalic sensory canals of the eelpout Austrolycus depressiceps (4.5–22.5 cm TL) across its latitudinal distribution in South Pacific (45°S–55°S). Geometric morphometric analyses show that the shape varied from individuals with larger snout and an extended suborbital canal to individuals with shorter snouts and frontally compressed suborbital canal. There was size variation across the sampled populations, but that size does not have a clear latitudinal gradient. Only 8% of the shape variation relates to this size variation (allometry), represented by a decrease in the relative size of the eye, and a depression of the posterior margin of the head. There were spatial differences in the shape of the head, but these differences were probably caused by allometric effects. Additionally, 2 of the canals of the cephalic lateralis pores and the head shape showed modularity in its development. This study shows that the morphology of marine fish with a shallow distribution varies across distances of hundreds of kilometers (i.e., phenotypic modulation).