The diverse deep-sea order Stomiiformes includes 457 species of mesopelagic and bathypelagic fishes with a remarkable diversity of structures associated with feeding, locomotion, and bioluminescence. This study investigates their patterns of body-shape evolution using geometric morphometry in an ecological and phylogenetic context. A total of 473 specimens from 56 different species in 48 genera representing all five families were photographed and 14 homologous landmarks and 50 semilandmarks were marked on the digital images. A principal component analysis (PCA) visualized body-shape variation, and morphological disparity analysis evaluated differences in variance among species in relation to their dietary classes, habitat partitioned by depth, and the presence or absence of diel vertical migration. The study also tested phylogenetic and ecological signals. The PCA revealed that variation in fin size and position, particularly for the dorsal and anal fins, accounted for the most important axis of variation among species. Changes in relative body size and body depth also contributed to morphological diversity. There is a trend toward body elongation in relation to depth distribution, with the meso-bathypelagic species having more elongated bodies than those restricted to the mesopelagic zone. Piscivorous and generalist species exhibit higher morphological disparity when compared to zooplanktivorous species, and meso- to bathypelagic species exhibit higher morphological disparity when compared to strictly mesopelagic species. A high phylogenetic signal indicates that morphological diversification within the Stomiiformes fits the expectations of Brownian evolution, in which the degree of shared ancestry rather than similarity of ecological niche predicts anatomical similarity. However, the current dataset may lack the statistical power to uncover any causal relationship between shifts in depth, diet, or migration and the shape diversification of stomiiforms.